Methods for diagnosing and treating inflammatory bowel disease

ABSTRACT

Methods and materials are disclosed for testing biomarkers in a subject suffering from inflammatory bowel disease (IBD) are described herein. Such detection can be useful for diagnosing and treating ulcerative colitis (UC) and Crohn&#39;s disease (CD), two forms of IBD that are otherwise difficult to distinguish. The method includes measuring the level of one or more of several biomarkers, including HD5 or MMP-7, which are expressed differentially in patents with UC and CD. A treatment may be based on the determination of whether the subject has ulcerative colitis or Crohn&#39;s disease.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.16/571,034, filed Sep. 13, 2019, which is a continuation ofPCT/US2018/024069 filed Mar. 23, 2018, which claims the benefit of U.S.Provisional Patent Application No. 62/475,506, filed Mar. 23, 2017, eachof which is relied upon for priority and incorporated by referenceherein in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grant numbersR21DK095186; U54CA091408-09S1; U54CA091408-0952; U54RR026140;U54MD007593; UL1RR024975; UL1TR000445; G12MD007586; U54CA163069; R24DA036420; and S10RR0254970 awarded by the National Institute of Health.The government has certain rights in the invention.

In this context “government” refers to the government of the UnitedStates of America.

BACKGROUND OF THE DISCLOSURE

Inflammatory bowel disease (“IBD”) is the chronic relapsing inflammationof all, or part of, the digestive tract. There are two types of IBD,ulcerative colitis (“UC”) and Crohn's disease (“CD”). Crohn's diseaseinvolving only colon is termed as Crohn's colitis (“CC”). Whennondefinitive evaluations have been established for criteria for eitherUC or CC are labeled as “indeterminate colitis (IC)”. UC results ininflammation and ulceration of the mucosal and, to a lesser degree, thesubmucosal linings of the colon and rectum. CC differs from UC in thatit may result in inflammation deeper within all the four colonic layers(transmural inflammation and skip lesions). Furthermore, CC may alsoaffect other organs through fistulation.

UC and CD affect an estimated 2 million people in the US alone withassociated annual health care costs of over $6.8 billion. While UC andCD are both types of IBDs, differences between patients having UC or CDhas major implications. Currently, clinicians use inexact combinedclassification for patients having IBD, which include clinical,endoscopy, radiological, and histopathology in an effort to diagnose CDand UC. Nonetheless, differentiating patients having UC or CD amongpatients suffering from IBD remains challenging, so much so that casesof patients having IBD that are difficult classify as UC or CD areclassified as having indeterminate colitis (“IC”). A significantsubgroup of IBD patients are misdiagnosed or have a correct diagnosisdelayed despite use of a state-of-the-art classification system applyingclinical, endoscopic, radiologic and histologic tools. Indeed, it isestimated that 30% of patients suffering from IBD cannot currently beaccurately diagnosed as CD or UC.

In addition, 15% of colonic IDB cases that undergo ileal pouch analanastomosis surgery, as they are diagnosed with UC, will subsequentlyhave their original diagnosis changed to CD based on their postoperativefollow-up visits, clinical and histopathology changes, and developmentof de novo CD in the ileal pouch. Ileal pouch anal anastomosis, atreatment normally suitable for UC but not CD, restores gastrointestinalcontinuity after surgical removal of the colon and rectum, and involvesthe creation of a pouch of small intestine to recreate the removedrectum.

Implications of distinguishing cases of UC and CD include choice ofmedical treatment, timing of surgery, prognosis, whether to offer thepatient an ileal pouch anal anastomosis, and lifestyle expectations. Forthese reasons, there is a need for improving the diagnosis, andsubsequent treatment, of subjects having IBD.

SUMMARY

It has been discovered that Paneth cells secreted DEFA5 also known asHD5 serve as biomarkers for determining whether a patient suffering fromIBD has UC or CD.

In a first aspect, a method of measuring DEFA5 (HD5) in a patientsuffering from or at risk of IBD is disclosed, said method comprising:obtaining a sample from the patient; and measuring at least one of theexpression of DEFA5 (HD5) and the concentration of DEFA5 (HD5) in thesample.

In a second aspect, a method of treating a patient suffering from or atrisk of IBD is disclosed, said method comprising: obtaining a samplefrom the patient; measuring at least one of the expression of DEFA5(HD5) and the concentration of DEFA5 (HD5) in the sample; and performingan intervention on the patient to treat one of Crohn's disease andulcerative colitis.

In a third aspect, a method of measuring MMP-7 in a patient sufferingfrom or at risk of IBD is disclosed, said method comprising: obtaining asample from the patient; and measuring at least one of the expression ofMMP-7 and the concentration of MMP-7 in the sample.

In a fourth aspect, a method of treating a patient suffering from or atrisk of IBD is disclosed, said method comprising: obtaining a samplefrom the patient; measuring at least one of the expression of MMP-7 andthe concentration of MMP-7 in the sample; and performing an interventionon the patient to treat one of Crohn's disease and ulcerative colitis.

In a fifth aspect, a method of measuring biomarkers in a patientsuffering from or at risk of IBD is disclosed, said method comprising:obtaining a sample from the patient; measuring at least one of theexpression of DEFA5 (HD5) and the concentration of DEFA5 (HD5) in thesample; and measuring at least one of the expression of MMP-7 and theconcentration of MMP-7 in the sample.

In a sixth aspect, a method of treating a patient suffering from or atrisk of IBD is disclosed, said method comprising: obtaining a samplefrom the patient; measuring at least one of the expression of DEFA5(HD5) and the concentration of DEFA5 (HD5) in the sample; measuring atleast one of the expression of MMP-7 and the concentration of MMP-7 inthe sample; and performing an intervention on the patient to treat oneof Crohn's disease and ulcerative colitis.

In a seventh aspect, a kit for measuring DEFA5 (HD5) and MMP-7 in asample is disclosed, the kit comprising: a first assay for measuring atleast one of the expression of human DEFA5 (HD5) and the concentrationof human DEFA5 (HD5) in a sample; and a second assay for measuring atleast one of the expression of human MMP-7 and the concentration ofhuman MMP-7 in a sample.

In an eighth aspect, a method of measuring a biomarker in a patientsuffering from or at risk of inflammatory bowel disease (IBD) isdisclosed, said method comprising: obtaining a sample from the patient;and measuring a level of the biomarker in the same, the level of thebiomarker selected from the group consisting of: the expression of thebiomarker, the activity of the biomarker, and the concentration of thebiomarker; wherein said biomarker is selected from Table 1.

The above methods may include diagnosing the patient as suffering fromCD if the level of DEFA5 (HD5) concentration or DEFA5 (HD5) expressionis greater than a given threshold level, diagnosing the patient assuffering from UC if the level of DEFA5 (HD5) concentration or DEFA5(HD5) expression is below a threshold level, or both.

The above methods may include diagnosing the patient as suffering fromCD if the level of MMP-7 concentration or MMP-7 expression is less thana given threshold level, diagnosing the patient as suffering from UC ifthe level of MMP-7 concentration or MMP-7 expression is above athreshold level, or both.

The above presents a simplified summary in order to provide a basicunderstanding of some aspects of the claimed subject matter. Thissummary is not an extensive overview. It is not intended to identify keyor critical elements or to delineate the scope of the claimed subjectmatter. Its sole purpose is to present concepts in a simplified form asa prelude to the more detailed description that is presented later.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B illustrate a comparison of new diagnoses according to anembodiment of an assay method of the present invention with previousattending physical diagnoses.

FIGS. 2A-H show differential expression and concentration of DEFA5 (HD5)in CC and UC subjects. 2A is a bar graph showing transcription levels ofDEFA5 (HD5) in subjects suffering from moderate UC as compared tomoderate CC. 2B is a western blot analysis of DEFA5 (HD5) levels indiverticulitis, UC, and CC subjects. 2C is a scatter plot graphquantifying the western blot DEFA5 (HD5) levels. 2D-G is histologicalstaining of DEFA5 (HD5) tissue samples from control, diverticulitis, UC,and CC subjects, respectively. 2H is a bar graph showing quantifiedDEFA5 (HD5) staining counts of UC and CC subjects as compared to thecontrol.

FIG. 3 is a bar graph showing differentially expressed MMP-7 in UCsubjects as compared to CC subjects.

FIG. 4 is a western blot analysis of MMP-7 levels in diverticulitis, UC,and CC subjects.

FIG. 5 is a plot graph quantifying the western blot MMP-7 levels of FIG.4.

FIGS. 6A-G show a series of plot graphs quantifying and comparingwestern blot DEFA5 (HD5) and MMP-7 levels in control, diverticulitis,UC, and CC subjects. 6A=diverticulitis, 6B=mild UC, 6C=moderate UC,6D=severe UC, 6E=mild CC, 6F=moderate CC, and 6G=severe CC.

FIG. 7 shows the sequence details of canonical human HD5 protein.

FIGS. 8A-D illustrate that it is possible to use DEFA5 (HD5) todetermine patient candidacy for IPAA. 8A=Representative results from aRPC-operated patient that did not change the diagnosis after surgery andwas molecularly tested using DEFA5 (HD5) IHC. 8B=Representative resultsfrom a UC RPC and IPAA operated patients that did change the diagnosisfrom UC to de novo Crohn's was molecularly tested using DEFA5 (HD5) IHC.C. NL-Ileum, control. 8D=Quantification of NEARAS DEFA5 (HD5) IHCstaining spot counts for UC RPC and IPAA-operated patients who did nothave their original diagnosis changed versus those who did change fromUC to de novo Crohn's. (Ctrl 1 Destaining control, UC=UlcerativeColitis, CC=Crohn's Colitis, DV=Diverticulitis, DVL=Diverticulosis).

FIGS. 9A-I illustrate H&E staining on parallel sections the typicalmorphological appearance of Paneth cell (PCs) including the presence ofdense apical eosinophilic granules. Upper panel: 9A, Diverticulitis (DV,no PCs), 9B, Diverticulosis (DVL, no PCs), 9C, Normal (NL-Colon,Control, no PCs). Middle panel: 9D, UC (found prodromal PC in onepatient, arrow). 9E, CC, demonstrate abundance of PCs allover colonicbasal crypts (arrows). 9F, Normal (NL-Ileum, Control), with abundance ofPCs. Lower panel: IHC detection of Paneth cell markers α-defensin 5(DEFA5) and lysozyme (LYZ) in the colon. 9G, NL-Colon, 9H, CC, and 9I,NL-Ileum, Control.

FIGS. 10A-J illustrate a double stain of PCs, lysosomes and DEFA5 (HD5).Double staining analyses from de novo Crohn's (10A and 10D), and normalileum/control (10G) are presented. Image deconvolutions are displayedvertically to evaluate lysozyme-specific permanent red (10B, 10E and10H) and HD5α-specific DAB (FIGS. 10C, 10F and 10I). The normal colonimage (FIG. 10J), which lacks PCs, was not further processed.

FIGS. 11A-D illustrate an assessment of DEFA5 (HD5) and Paneth cells ininflamed and normal, adjacent tissue. DEFA5 (HD)5 staining of CCinflamed and normal, adjacent tissue shows expression of DEFA5 (HD5) inall patient samples examined (FIG. 11A), compared to inflamed andadjacent, normal tissue of UC patients (FIG. 11B).H&E stains for PanethCells (FIGS. 11C and 11D), were negative for PCs in all tissues.

FIGS. 12A-D show histological staining of colon tissue in varioussubjects. 12A=CC, 12B=UC, 12C=diverticulitis, 12D=normal colon.

FIG. 13 illustrates the results of an antibody specificity assay. Dotblots were performed on recombinant HD1-6 with various commercialantibodies to determine specificity to HD5. Ponceau S Stain is used as aloading control. We found that the antibody from Santa Cruz was the mostspecific for DEFA5 (HD5) of those tested.

FIG. 14 is a condensed list of the samples included in all experimentsand the colon locations from which the samples were taken.

FIG. 15 shows an assessment of levels of HD5 in surgical pathologycolectomy samples via IHC in patients described in FIG. 1A.

DETAILED DESCRIPTION Definitions

Unless otherwise defined, all terms (including technical and scientificterms) used herein have the same meaning as commonly understood by oneof ordinary skill in the art of this disclosure. It will be furtherunderstood that terms, such as those defined in commonly useddictionaries, should be interpreted as having a meaning that isconsistent with their meaning in the context of the specification andshould not be interpreted in an idealized or overly formal sense, unlessexpressly so defined herein. Well-known functions or constructions maynot be described in detail for brevity or clarity.

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting. As used herein, thesingular forms “a”, “an”, and “the” are intended to include the pluralforms as well, unless the context clearly indicates otherwise.

The term “consisting essentially of” means that, in addition to therecited elements, what is claimed may also contain other elements(steps, structures, ingredients, components, etc.) that do not adverselyaffect the operability of what is claimed for its intended purpose asstated in this disclosure. This term excludes such other elements thatadversely affect the operability of what is claimed for its intendedpurpose as stated in this disclosure, even if such other elements mightenhance the operability of what is claimed for some other purpose.

The terms “about” and “approximately” shall generally mean an acceptabledegree of error or variation for the quantity measured given the natureor precision of the measurements. Typical, exemplary degrees of error orvariation are within 20%, preferably within 10%, and more preferablywithin 5% of a given value or range of values. For biological systems,the term “about” refers to an acceptable standard deviation of error,preferably not more than 2-fold of a given value. Numerical quantitiesin this detailed description are approximate unless stated otherwise,meaning that the term “about” or “approximately” can be inferred whennot expressly stated.

The terms “individual”, “subject”, or “patient” as used herein refer toany animal, including mammals, such as mice, rats, other rodents,rabbits, dogs, cats, swine, cattle, sheep, horses, primates, and humans.The terms may specify male or female or both, or exclude male or female.

The terms “treatment”, “treat”, and “treating”, as used herein, refer toa course of action (such as administering a compound or pharmaceuticalcomposition) initiated after the onset of a clinical manifestation of adisease state or condition so as to eliminate or reduce such clinicalmanifestation of the disease state or condition. Such treating need notbe absolute to be useful.

The terms “first”, “second”, and the like are used herein to describevarious features or elements, but these features or elements should notbe limited by these terms. These terms are only used to distinguish onefeature or element from another feature or element. Thus, a firstfeature or element discussed below could be termed a second feature orelement, and similarly, a second feature or element discussed belowcould be termed a first feature or element without departing from theteachings of the present disclosure.

Methods of Treatment and Diagnosis

An assay method of diagnosing UC and CD in a subject, such as a human,suffering from IBD is described. The method measures DEFA5 (HD5) intissue taken from a subject having IBD. DEFA5 (HD5) is a small,microbicidal innate immune system protein belonging to the alphadefensing family of mammalian defensing peptides. DEFA5 (HD5) isexpressed in various tissues and particularly on mucosal surfaces. DEFA5(HD5) is encoded by the gene DEFA5. DEFA5 (HD)5 is involved in hostdefense mechanisms, and is highly expressed in secretory granules ofPaneth cells of the small intestine (ileum). Like most secretedproteins, HD5 is synthesized as prepro-HD5 (1-94) that undergoesproteolytic processing first, to the inactive pro-HD5s (20-94), HD5(23-94) and HD5 (29-94). HD5 (23-94) and HD5 (29-94) are found withintissues, while HD5 (20-94) is the predominant intracellular form. Thepro-HD5s are then processed to two active or mature forms. HD5 (56-94)and HD5 (63-94) with HD5 (63-94) being the most abundant form. Thesemature forms of HD5 are cysteine-rich host defense peptides which exerta broad-spectrum antimicrobial activity and contribute to innateimmunity in the human gut. As used herein, HD5 may refer to exclusivelymature forms or inactive forms of HD5.

Matrix metalloproteinase-7 (MMP-7, encoded by the MMP7 gene) isresponsible for cleaving and activating HD5. It is believed that theremay be a dysfunction in the activation pathway of HD5 in patientssuffering from moderate and severe CD, and thus, an excess amount ofinactive form HD5 is a potential mechanism for inflammation in patientssuffering from CD. This excessive amount of inactive form HD5 may causeincreased damage to the epithelial lining and potentially even adysregulation in the levels and make-up of gut flora. The canonicalstructure of human MMP-7 is a 54 residue polypeptide (see Uniprotaccession number A5GZ72).

The sample can be taken from any suitable source for measuring HD5concentration, HD5 expression levels, MMP-7 expression, or MMP-7concentration, such as the tissue samples from the large intestine orrectum. In this disclosure the term “expression of HD5” should beinterpreted to mean the expression of the DEFA5 gene; “levels of HD5”should be interpreted to mean the concentration of HD5; “expression ofMMP-7” should be interpreted to mean the expression of the MMP7 gene;“levels of MMP-7” should be interpreted to mean the concentration ofmatrix metalloproteinase-7.

The sample may be taken from a subject who is suffering from or at riskof IBD. The subject may display one or more symptoms characteristic ofIBD, such as severe diarrhea, abdominal pain, fatigue, and weight loss.In some embodiments of the method, the subject displays more than one ofsaid symptoms. In further embodiments the subject displays 2, 3, or 4 ofsaid symptoms.

It has been discovered that the genes encoding HD5 and MMP-7 aredifferentially expressed in subjects having UC and CD; and further, thatthe concentration of HD5 is significantly higher in tissues of CDpatients than in UC patients. Used in this way, HD5 and MMP-7concentrations, and HD5 expression and MMP-7 expression, can be utilizedand measured as biomarkers for distinguishing UC and CD in patientshaving IBD. This can in turn be used to more effectively treat thesubject. For example, as ileal pouch anal anastomosis is clinically muchmore successfully in patients having UC than in patients suffering fromCD, patients identified as having levels of HD5 or MMP-7 levelsindicative of UC, or not having CD, may be treated with ileal pouch analanastomosis. Indeed, as HD5 is produced by Paneth cells only, one wouldnot typically expect to find Paneth cells that secret HD5 in the colon.The inventors have discovered Paneth cells (secreting HD5) areabundantly found in subjects having UC. On the other hand, patientsidentified as having levels of HD5 or MMP-7 and HD5 or MMP-7 expressionindicative of CD may be treated with any suitable treatment for CD. Inan embodiment, a diagnosing step, such as diagnosing a subject with UCor CD, is optional.

The methods may include a step of comparing the level of the biomarkerin question to a benchmark value. The benchmark value may be a measureof central tendency based on levels observed in one or more populationsof subjects that are established to be unafflicted by either of UC orCD. For example, the benchmark value may be a mean level of the geneexpression or protein concentration observed in samples from apopulation of subjects who are unafflicted by UC, unafflicted by CD, orboth. The population may be defined by one or more of the patient'sgeography, age, ethnicity, sex, and medical history. The benchmark valuemay take into account a measure of variation combined with a measure ofcentral tendency. For example, the benchmark value may be a mean levelof the gene expression or protein concentration observed in a giventumor population, plus or minus a margin of error. The benchmark may bebased on raw measurements (such as fragments of mRNA or cDNA per kb genelength per million reads) or normalized measurements (such as % ofnormal expression, or expression compared to a constitutively expressedor widely expressed gene with generally consistent expression, such asβ-actin).

The benchmark may also be established by analysis of a control samplethat is measured alongside the sample from the subject. Examples ofsuitable control samples are: a sample from a subject unafflicted withUC, a sample from a subject unafflicted with CD, a sample from a subjectafflicted with UC (although unafflicted with CD), a sample from asubject afflicted with CD (although unafflicted with UC), a sample froma subject afflicted with diverticulitis (although unafflicted witheither of UC or CD), and a sample from a subject unafflicted from IBD.

In an embodiment, an assay method of differentially diagnosing UC and CDin a patient suffering from IBD includes measuring the level of HD5 orMMP-7 or HD5 or MMP-7 expression present in a sample obtained from thepatient. The level of HD5 or MMP-7 concentration or expression in thetissue may be measured by any suitable peptide analysis. For example,the measuring step may include one or more of enzyme-linkedimmunosorbent assay (ELISA), cation-ion exchange, NMR analysis,genome-wide transcriptome analysis, and mass spectrometry. The methodmay include comparing the concentration or expression of the biomarkerin the sample to the benchmark, and making a diagnosis if theconcentration or expression of the biomarker in the sample issignificantly less than or significantly greater than the benchmarkvalue. For the example, the method may comprise comparing theconcentration or expression of HD5 in the sample to the benchmark, andmaking a diagnosis of CD if the concentration or expression of HD5 inthe sample is significantly greater than the benchmark value. As anotherexample, the method may comprise comparing the concentration orexpression of HD5 in the sample to the benchmark, and making a diagnosisof UC if the concentration or expression of HD5 in the sample is notsignificantly greater than the benchmark value. As another example, themethod may comprise comparing the concentration or expression of MMP-7in the sample to the benchmark, and making a diagnosis of UC if theconcentration or expression of MMP-7 in the sample is significantlygreater than the benchmark value. As another example, the method maycomprise comparing the concentration or expression of MMP-7 in thesample to the benchmark, and making a diagnosis of CD if theconcentration or expression of MMP-7 in the sample is not significantlygreater than the benchmark value. In a further example, the methodcomprises measuring the concentration or expression of both MMP-7 andHD5, and making a diagnosis of either: CD if the concentration orexpression of MMP-7 in the sample is not significantly greater than thebenchmark value and the concentration or expression of HD5 issignificantly greater than the benchmark value; or UC if theconcentration or expression of MMP-7 in the sample is significantlygreater than the benchmark value and the concentration or expression ofHD5 is not significantly greater than the benchmark value.

The difference in expression or concentration may be consideredsignificant based on any of a variety of known statistical tests forsignificance. These are generally based on a collection of measurementsmade from a sampled population, and are affected by both the populationsize and the sampling size. Such statistical tests are well known in theart and are not further elaborated upon in this disclosure; outsidereferences can be relied upon to enable those skilled in the art todetermine statistical significance, such as Rosener's Fundamentals ofBiostatistics, 8^(th) ed. (2015), Cengage Learning, Boston, Mass.

The method may include diagnosing the patient as having UC if HD5 or HD5expression is at any level that is indicative of a patient not havingCD, such as less than 5× normal levels of HD5 (i.e., levels of HD5typical of a subject unafflicted with CD), less than about 5×-30× normallevels of HD5 or HD5 expression, less than about 31× normal levels, orless than about 118× normal levels. In a further embodiment, the patientis diagnosed as having UC if HD5 expression is at a level of less than10⁶, 10⁷, 1.9×10⁷, 6×10⁵, or 3×10⁶ HD5 mRNA transcript per 10 ng RNA. Insome embodiments of the method the patient may be diagnosed as having CDif the level of HD5 expression is at any level indicative of a patienthaving CD, such as at least 3×10⁶, 10⁷, 1.9×10⁷, 7×10⁷, 10⁸, 1.2×10⁸, orfrom about to 3×10⁶ to 1.2×10⁸ HD5 mRNA Transcript per 10 ng RNA. Thediagnosing may diagnose the patient as having CD if the patient has aMMP-7 concentration or MMP-7 expression level indicative of a patienthaving CD, such as up to a threshold limit that is 10× a benchmark valueof MMP-7 concentration or MMP-7 expression. In further embodiments, thediagnosis may be CD using a threshold limit of up to 5×, and up to 1× abenchmark value. As used herein, a “normal level” of HD5 or HD5expression means a level of HD5 or HD5 expression in the digestive tracttissue from a subject not having CD or UC, or a subject suffering fromIBD and specifically UC. Normal HD5 expression may refer to from 1×10⁵to 9×10⁵ HD5 mRNA Transcript per 10 ng RNA, or about 6×10⁵ HD5 mRNATranscript per 10 ng RNA. As used herein, a “normal level” of MMP-7 orMMP-7 expression means a level of MMP-7 or MMP-7 expression in thedigestive tract tissue from a subject not having CD or UC, or a subjectsuffering from IBD, specifically CD.

In another embodiment, an assay method for differentially diagnosing UCand CD in a patient suffering from, or at risk of, IBD includesmeasuring the level of MMP-7 or MMP-7 expression present in a sampleobtained from the patient. The level of MMP-7 or MMP-7 expression in thetissue may be measured by any suitable peptide analysis. In anembodiment, the method of diagnosing may be performed ex vivo.

In one embodiment, the assay methods involve determining the status of asubject with respect to the activity and/or expression of HD-5 or MMP-7or the activity and/or expression of a polypeptide regulated by HD-5 orMMP-7. In one embodiment, such methods comprise determining the level ofexpression or activity of HD-5 or MMP-7 or a polypeptide regulated byHD-5 or MMP-7 in a sample from the subject. The method may furthercomprise collecting the sample from the subject. As used herein, abiological sample which is subjected to testing is a sample derived froma subject and includes, but is not limited to, any biological material,such as a bodily fluid. Examples of bodily fluids include, but are notlimited to, whole blood, serum, saliva, tissue infiltrate, pleuraleffusions, lung lavage fluid, bronchoalveolar lavage fluid, and thelike. The biological fluid may be a cell culture medium or supernatantof cultured cells. For example, the sample can be a blood sample or aserum sample. As another example the sample may be tissue or fluids fromthe subject's digestive tract. Some embodiments of the method involve asample of intestinal tissue. In specific embodiments, the biologicalsample is collected from the colon of a subject (such as colonic tissue)or the ileum of a subject (such as ileal tissue).

Some embodiments of the method comprise measuring the concentration ofthe biomarker protein by selectively staining or dying the sample formthe subject and measuring the signal from the stain. The stain or dyemay comprise an antibody or an antibody fragment to recognize theprotein. The stain or dye may also comprise a reporter, such acolorimetric group, a radionuclide, a stable isotope, a fluorophore, achromophore, an enzyme, a magnetic particle, and a quantum dot. Theconcentration of the protein can then be measured by observing thesignal from the reporter, such as by microscopy, colorimetry,radiometry, fluoroscopy, magnetotaxis, or any combination of theforegoing. In a specific embodiment of the method, the concentration ofHD5 or MMP-7 is measured by immunostaining the sample with animmunostain that recognizes the biomarker and counting the number ofstained cells by microscopy. This approach has the advantage of relativesimplicity, and only requires the types of equipment that are alreadypresent in typical clinical laboratories. In specific examples in whichthe biomarker is HD5, a diagnosis can be made based on a thresholdnumber of cells that stain positive, such as 10%, 20%, and 30%. If thenumber of HD5 stained cells is significantly above the threshold value,than a diagnosis of CD can be made; whereas if the number of HD5 stainedcells is significantly below the threshold value, than a diagnosis of UCcan be made.

Those subjects in which HD-5 or MMP-7 activity and/or expression differs(increased or decreased) from a control or benchmark value or theactivity of a polypeptide regulated by HD-5 or MMP-7 differs as comparedto a control or benchmark value are determined to be suffering from orat risk for a disease states and conditions associated with orcharacterized by increased or decreased HD-5 or MMP-7 activity.

Assay techniques that can be used to determine levels of expression oractivity in a sample are known. Such assay methods include, but are notlimited to, radioimmunoassays, reverse transcriptase PCR (RT-PCR)assays, immunohistochemistry assays, in situ hybridization assays,competitive-binding assays, Western Blot analyses, ELISA assays andproteomic approaches, two-dimensional gel electrophoresis (2Delectrophoresis) and non-gel based approaches such as mass spectrometryor protein interaction profiling. Assays also include, but are notlimited to, competitive and non-competitive assay systems usingtechniques such as radioimmunoassays, enzyme immunoassays (EIA), enzymelinked immunosorbent assay (ELISA), sandwich immunoassays, precipitinreactions, gel diffusion reactions, immunodiffusion assays,agglutination assays, complement-fixation assays, immunoradiometricassays, fluorescent immunoassays, protein A immunoassays, andimmunoelectrophoresis assays. For examples of immunoassay methods, seeU.S. Pat. Nos. 4,845,026 and 5,006,459.

In an ELISA assay, an antibody is prepared, if not readily availablefrom a commercial source, specific to an antigen, such as, for example,HD-5 or MMP-7 or a polypeptide regulated by HD-5 or MMP-7. In addition,a reporter antibody generally is prepared. The reporter antibody isattached to a detectable reagent such as a radioactive, fluorescent, orenzymatic reagent, for example horseradish peroxidase enzyme or alkalinephosphatase. In one embodiment of the ELISA, to carry out the ELISA,antibody specific to the antigen is incubated on a solid support thatbinds the antibody. Any free protein binding sites on the dish are thencovered by incubating with a non-specific protein. Next, the sample tobe analyzed is incubated with the solid support, during which time theantigen binds to the specific antibody. Unbound sample is washed outwith a buffer. A reporter antibody specifically directed to the antigenand linked to a detectable reagent is introduced resulting in binding ofthe reporter antibody to any antibody bound to the antigen. Unattachedreporter antibody is then washed out. Reagents for detecting thepresence of the reporter antibody are then added. The detectable reagentis then determined in order to determine the amount of antigen present.In an alternate embodiment, the antigen is incubated with the solidsupport, followed by incubation with one or more antibodies, wherein atleast one of the antibodies comprises a detectable reagent. Quantitativeresults may be obtained by reference to a standard curve.

Optionally, a genetic sample from the biological sample can be obtained.The genetic sample comprises a nucleic acid, preferably RNA and/or DNA.For example, in determining the expression of genes mRNA can be obtainedfrom the biological sample, and the mRNA may be reverse transcribed intocDNA for further analysis. Alternatively, the mRNA itself is used indetermining the expression of genes. A genetic sample may be obtainedfrom the biological sample using any techniques known in the art(Ausubel et al. Current Protocols in Molecular Biology (John Wiley &Sons, Inc., New York, 1999); Molecular Cloning: A Laboratory Manual, 2ndEd., ed. by Sambrook, Fritsch, and Maniatis (Cold Spring HarborLaboratory Press: 1989); Nucleic Acid Hybridization (B. D. Hames & S. J.Higgins eds. 1984) each of the foregoing being incorporated herein byreference). The nucleic acid may be purified from whole cells using DNAor RNA purification techniques. The genetic sample may also be amplifiedusing PCR or in vivo techniques requiring subcloning. The genetic samplecan be obtained by isolating mRNA from the cells of the biologicalsample and reverse transcribing the RNA into DNA in order to create cDNA(Khan et al. Biochem. Biophys. Acta 1423:17 28, 1999).

Once a genetic sample has been obtained, it can be analyzed. Theanalysis may be performed using any techniques known in the artincluding, but not limited to, sequencing, PCR, RT-PCR, quantitativePCR, restriction fragment length polymorphism, hybridization techniques,Northern blot, microarray technology, and similar techniques. Indetermining the expression level of a gene or genes in a genetic sample,the level of expression may be normalized by comparison to theexpression of another gene such as a well-known, well characterized geneor a housekeeping gene (for example, actin). For example,reverse-transcriptase PCR (RT-PCR) can be used to detect the presence ofa specific mRNA population in a complex mixture of thousands of othermRNA species. Hybridization to clones or oligonucleotides arrayed on asolid support (e.g., gridding) can be used to both detect the expressionof and quantitate the level of expression of that gene. In thisapproach, a cDNA encoding an antigen is fixed to a substrate. Thesubstrate may be of any suitable type including but not limited toglass, nitrocellulose, nylon, or plastic. At least a portion of the DNAencoding the antigen is attached to the substrate and then incubatedwith the analyte, which may be RNA or a complementary DNA (cDNA) copy ofthe RNA, isolated from the sample of interest. Hybridization between thesubstrate bound DNA and the analyte can be detected and quantitated byseveral means including but not limited to radioactive labeling orfluorescence labeling of the analyte or a secondary molecule designed todetect the hybrid. Quantitation of the level of gene expression can bedone by comparison of the intensity of the signal from the analytecompared with that determined from known standards. The standards can beobtained by in vitro transcription of the target gene, quantifying theyield, and then using that material to generate a standard curve.

The method may include diagnosing the patient as having UC if MMP-7concentration or MMP-7 expression is at any level indicative of apatient having UC, such as from 2×-100×, 10×, 2×-50×, 5×-15×, or about10× normal MMP-7 concentration or MMP-7 expression levels. In someembodiments of the method, the patient may be diagnosed as having CD ifthe MMP-7 concentration or MMP-7 expression is at any level indicativeof a patient having CD, such as less than 1×-10× or 2×-5× normal levelsof MMP-7 or MMP-7 expression.

A method of treating IBD in a patient suffering from IBD may include:(a) measuring the level of HD5 or HD5 expression present in a sampleobtained from the patient, said measuring step optionally comprising oneof cation-ion exchange, NMR analysis, genome-wide transcriptomeanalysis, and mass spectrometry, whereby a level of HD5 or HD5expression is obtained; (b) if the level of HD5 or HD5 expression is ata level indicative of a patient not having CD, treating the IBD in thepatient with a suitable medical treatment for UC; if the level of HD5 orHD5 expression is at a level indicative of a patient having CD, treatingthe IBD in the patient with a suitable medical treatment for CD. Inanother embodiment, levels of MMP-7 or MMP-7 expression are measuredrather than levels of HD5 to determine whether to treat UC or CD.

Suitable medical treatments for UC include ileal pouch anal anastomosisor the administration of pharmaceutical agents or salts thereof.Suitable pharmaceutical agents may be one or more of: an ironsupplement; an oral 5-aminosalicylate, such as mesalamine, balsalazideand olsalazine; an anti-inflammatory; a corticosteroid; animmunosuppressant such as azathioprine, mercaptopurine, methotrexate,and cyclosporine; an anti-TNF-alpha antibody such as infliximab,adalimumab, and golimumab; an anti-α4-integrin antibody such asvedolizumab; and an antibacterial antibiotic, such as ciprofloxacin andmetronidazole. Surgeries that are sometimes used to treat UC include aproctocolectomy, and an ileal pouch anal anastomosis. Note that ilealpouch anal anastomosis are recognized as relatively ineffective whenused to treat CD, in contrast to UC. It should also be noted thatcyclosporine and golimumab, while currently approved for the treatmentof UC in the United States, are not currently approved for the treatmentof CD. Some embodiments of the method involve performing an interventionthat is effective to treat UC, but either ineffective to treat CD or notyet approved by regulatory authorities for the treatment of CD.

Suitable medical treatments for CD include the administration ofpharmaceutical agents or salts thereof. Suitable pharmaceutical agentsinclude: an oral 5-aminosalicylate, such as mesalamine; a vitaminsupplement, such as a vitamin B-12 supplement and a vitamin Dsupplement; a mineral supplement, such as a calcium supplement; ananti-inflammatory; a corticosteroid such as prednisone and budesonide;an immunosuppressant such as azathioprine, tacrolimus, methotrexate, andmercaptopurine; an anti-TNF-α antibody, such as infliximab, adalimumab,and certolizumab pegol; an anti-α-4-integrin antibody, such asnatalizumab and vedolizumab; an anti-interleukin antibody, such asustekinumab; and an antibacterial antibiotic, such as metronidazole, andciprofloxacin. Although certolizumab pegol, methotrexate, andnatalizumab are approved in the US for the treatment of CD, they are notcurrently approved for the treatment of UC. Surgical approaches aresometimes used to treat severe cases of CD. Such surgeries includeostomy, colostomy, ileostomy, bowel resection, colectomy,proctocolectomy, and strictureplasty. In some embodiments of the method,the subject is treated using a diet that is advantageous for themanagement of CD, but not necessarily advantageous in the management ofUC. One such diet is a low fat diet. Some embodiments of the methodinvolve performing an intervention that is effective to treat CD, buteither ineffective to treat UC or not yet approved by regulatoryauthorities for the treatment of UC.

In an embodiment, the level of HD5 or HD5 expression may be elevatedabove normal levels in patients who are likely to be diagnosed UC but,at the time the HD5 or HD5 expression level is measured, diagnosed ashaving IC. These patients may be treated with any suitable medicaltreatments for UC.

A kit is provided for measuring HD5 in a subject. The kit may include adetectable antibody that is capable of binding with HD5. The antibodymay be capable of binding with HD5 yet not bind with other defensins,such as HD4 and HD5. The antibody may be a purified HD5-specificmonoclonal or polyclonal antibody, such as the HDAC5 Antibody fromGenWay Biotech, Inc. FIG. 7 shows the amino acid sequence of HD5,including a schematic showing HD5 antibody epitopes to distinguishpro-HD5 from mature HD5. FIG. 7 also shows the alignment of the primarysequence of HD5 with that of HD1 showing the differences between the twopolypeptides. The methods herein can involve detecting any proteinhaving the consensus sequence of HD5 such as to account for naturalvariation of HD5 in humans having different HD5 sequences.

A kit is provided for measuring HD5 and MMP-7 in a subject. The kit mayfind use in several of the methods provided above, as well as others.The kit may be, for example, used for the diagnosis of inflammatorybowel disease. The kit comprises an assay for measuring at least one ofHD5 concentration and HD5 expression; and an assay for measuring atleast one of MMP-7 concentration and MMP-7 expression.

FIG. 12 illustrates a histological staining of colon tissue in a subjecthaving CC. FIG. 12B illustrates a histological staining of colon tissuein a subject having UC. FIG. 12C illustrates a histological staining ofcolon tissue in a subject having Diverticulitis. FIG. 12D illustrates ahistological staining of colon tissue in a subject having a normalcolon.

Working Example 1

Abstract

Inability to distinguish Crohn's colitis from ulcerative colitis leadsto the diagnosis of indeterminate colitis. This greatly effects medicaland surgical care of the patient because treatments for the two diseasesvary. Approximately 30 percent of inflammatory bowel disease patientscannot be accurately diagnosed, increasing their risk of inappropriatetreatment. We sought to determine whether transcriptomic patterns couldbe used to develop diagnostic biomarker(s) to delineate inflammatorybowel disease more accurately. Four patients groups were assessed viawhole-transcriptome microarray, qPCR, Western blot, andimmunohistochemistry for differential expression of Human α-Defensin-5.In addition, immunohistochemistry for Paneth cells and Lysozyme, aPaneth cell marker, was also performed. Aberrant expression of Humanα-Defensin-5 levels using transcript, Western blot, andimmunohistochemistry staining levels was significantly upregulated inCrohn's colitis, p<0.0001. Among patients with indeterminate colitis,Human α-Defensin-5 is a reliable differentiator with a positivepredictive value of 96 percent. We also observed abundant ectopic cryptPaneth cells in all colectomy tissue samples of Crohn's colitispatients. In a retrospective study, we show that Human α-Defensin-5could be used in indeterminate colitis patients to determine if theyhave either ulcerative colitis (low levels of Human α-Defensin-5) orCrohn's colitis (high levels of Human α-Defensin-5). Twenty of 67patients (30 percent) who underwent restorative proctocolectomy fordefinitive ulcerative colitis were clinically changed to de novo Crohn'sdisease. These patients were profiled by Human α-Defensin-5immunohistochemistry. All patients tested strongly positive. Inaddition, we observed by both hematoxylin and eosin and Lysozymestaining, a large number of ectopic Paneth cells in the colonic crypt ofCrohn's colitis patient samples. Our experiments are the first to showthat Human α-Defensin-5 is a potential candidate biomarker tomolecularly differentiate Crohn's colitis from ulcerative colitis, toour knowledge. These data give us both a potential diagnostic marker inHuman α-Defensin-5 and insight to develop future mechanistic studies tobetter understand crypt biology in Crohn's colitis.

Methods

Clinical Samples and Ethical Consideration

In order to carryout tissue profiling of differentially expressedproteins/genes in IBD, we first sought ethical approval from the MeharryMedical College (IRB file #: 100916AM206) and Vanderbilt UniversityMedical Center (IRB file #s: 080898 and 100581) Institutional ReviewBoards [20]. Informed consent was provided, and patient participation inthe study was voluntary. Patient samples comprised of surgical pathologycolectomy tissues from adults with definitive UC and CC phenotypes aswell as those diagnosed with IC at Vanderbilt University Medical Center(VUMC) between 2000 and 2007. The full thickness surgical samples ofcolectomy tissue were analyzed by pathology teams at MMC and VUMC,Schools of Medicine following established protocol criteria for IBDsubtypes. For each selected sample, medical records data on patientdemographics, preoperative variables prior to and after time of ilealpouch-anal anastomosis surgery, surveillance endoscopic and clinicalfindings, and medical and surgical treatment history were reviewedretrospectively. Samples included in all experiments were taken fromvarious parts of the colon; all inflamed tissue unless otherwiseindicated. A condensed list of samples and colon locations are includedin Table 3, as shown in FIG. 13.

Diagnostic Criteria for Inflammatory Bowel Disease

Pathology teams at MMC and VUMC Schools of Medicine used the followingprotocol criteria for the final surgical pathology reporting.

For ulcerative colitis. Characteristic pattern of involvement of colon,worse distally in untreated patients; lack of perianal or fistulizingdisease; no granulomas, except in association with ruptured/injuredcrypts; no transmural lymphoid aggregates or other transmuralinflammation; no involvement of terminal ileum, except mild “backwashileitis” in cases with severe cecal involvement and no pyloricmetaplasia in terminal ileum.

For Crohn's disease. Involvement of other sites in the gastrointestinaltract (skip lesions, segmental disease); perianal or fistulizingdisease; granulomas, not in association with ruptured/injured crypts andterminal ileum involvement.

For indeterminate colitis. Distribution favors UC, but focal transmuralinflammation, or inflammation in ileum more than expected in backwashileitis and no fistulizing disease.

Vanderbilt Patient Medical Records Database

The availability of a detailed IBD patient database registry atVanderbilt University Medical Center (VUMC) made chart review andfollow-up surveillance possible. Medical records data on patientdemographics, preoperative variables prior to and after IPAA surgery,surveillance of endoscopic and clinical findings, and medical andsurgical treatment history were retrieved retrospectively.

Indeterminate Colitis Clinical Retrospective Study

A retrospective investigation was conducted to identify a cohort ofpatients diagnosed with IC and registered in the IBD Center at VUMC.Twenty-one patients, initially classified as IC at the time of diagnosisbetween years 2000-2007, were identified and reevaluated for diseasecourse in 2014, after a mean surveillance follow-up of 8.7±3.7 (range,4-14) years, in order to identify the rates of diagnosis resolution toUC or CC. Diagnosis for each patient was determined based on standardclinical and pathologic features as previously described [21,22].

Three gastrointestinal pathologists blinded to clinical diagnosisreconciled and confirmed colitis diagnosis for each patient andrepresented a consensus among treating physicians. Patients whoclinically did not changed and maintained the IC diagnosis were testedvia IHC and Nikon Element Advanced Research Analysis Software (NEARAS)for HD5 levels to determine if HD5 could be used to identify CC from UC.

Restorative Proctocolectomy Operated Patients' Retrospective Study

One hundred twenty patients with definitive UC underwent RPC surgerybetween Apr. 18, 2001 and Jun. 18, 2008. Of the 120 patients, 67 hadtheir diagnosis re-evaluated after a mean follow up of 9.4 (range, 6-13)years of functionally acceptable pouches. Compiled medical recordsallowed us to re-evaluate a progressive course of UC patients followingRPC. Clinical information needed for each of these patients wasavailable in the IBD medical records registry database at VUMC. The aimwas to reevaluate patients who underwent RPC operation for definitive UCand had a change in diagnosis to de novo Crohn's ileitis. Patients whohad a change in diagnosis should reconcile the molecular biometric testthat delineates IC into CC; again using NEARAS for HD5 levels.

cDNA Microarray

We performed a whole-transcriptome microarray with RNA extracted andpooled from human full thickness colon samples from UC and CC patients(n=5/group) (Affymetrix, Santa Clara, Calif.).

NanoString nCounter Human Inflammation Kit Gene Expression

RNA from UC and CCI tissue (and diverticulitis tissue used as a control)was processed by NanoString (NanoString Technologies Inc., Seattle,Wash.) to determine gene expression level according to the manufacturerprotocol [23].

Real-Time RT-PCR

Real-Time RT-PCR was used to measure transcript levels of HD5. RNA wasextracted from three human colon biopsy samples each from moderate UCand CC, and diverticulitis (DV) as a non-IBD control (RNeasy MiniprepKit, Qiagen, CA). cDNA was generated using iScript cDNA synthesis kit(Bio-Rad, Hercules, Calif.). Pre-designed TaqMan probes (Thermo FisherScientific, Waltham, Mass.) were purchased for HD5 and GAPHD control,and all samples were run in triplicate using a CFX96 qPCR thermocycler(Bio-Rad). Data were analyzed per the ΔΔCt method of analysis.

Western Blot and Immunohistochemistry

Western blot was used to assess any differences in HD5 protein levels.Protein was extracted from a minimum of 10 colon biopsy samples eachfrom mild, moderate, and severe UC; mild, moderate, and severe CC; andnon-IBD DV control. Whole cell lysates were extracted fromfull-thickness colon samples using T-PER (Thermo Fisher Scientific) permanufacturer's protocol. Bradford Assays (Bio-Rad) were run to determineprotein concentration, and protein was loaded onto a 4-20% SDS-PAGEtris/glycine gel (Bio-Rad). Proteins were transferred to PVDF (Bio-Rad),and Western blots for HD5 and β-actin loading control were performedwith primary and secondary antibodies (Santa Cruz, Dallas, Tex.) permanufacturer's protocol. Blots were visualized with Opti-4CNcolorimetric detection kit (Bio-Rad) and imaged with ChemiDocXRS+imaging system (Bio-Rad). Band intensities were measured and dataanalysis performed with Image Lab Software (Bio-Rad).

Five colon tissue protein extracts and staining of HD5 per disease byimmunohistochemistry (IHC) was done as previously described.24Quantification of HD5 staining was analyzed manually by microscopy andautomatically quantified using Nikon's Eclipse Ti microscope withbuilt-in NEARAS [24,25].

NEARAS Technology for Quantification of Immunohistochemistry Staining

NEARAS (Melville, N.Y.) was used to calculate the number of cells withHD5 staining in IHC tissue. A mean intensity threshold of 20 to 255intensity units was established to eliminate a false-positive signalfrom background staining. A circularity parameter of 0.5 to 1 andequivalent diameter of 5-15 micrometer was used to select for cells. Allthreshold parameters were used in each image to count the number ofHD5-positive cells in tissue samples.

Statistical Analysis

The Vanderbilt University Microarray Core Laboratory performedstatistical analyses for the microarray. Transcriptome level foldchanges and the significance of those changes were calculated using oneway ANOVA with Bonferroni's correction for multiple comparisons.Significantly changed transcripts were defined as having >2.0 foldexpression change from controls and a Benjamini-Hochberg (BH) falsediscovery rate corrected ANOVA p-value <0.05. All other statisticalanalyses were performed using GraphPad Prism v6 software [26]. qRT-PCRand IHC HD5 counts were examined by applying an unpaired two-tailedStudent's t-test with the Welch correction, respectively. Western blotswere analyzed by ANOVA followed by Fisher's test for multiplecomparisons. Chi square tests were utilized for determining relatednessof HD5 levels to CC. For all statistical analyses, p<0.05 indicated astatistical significance.

Dual Staining of Human α-Defensin-5 and Lysozyme

DoubleStain IHC was performed on a Lab Vision autostainer 360 (Thermofisher) using Abcam's M&R on human tissue (DAB & AP/Red) staining kit(ab210059, Abcam Biotechnology, Cambridge, UK). The manufacture'srecommended conditions were used with the following modifications. Themouse anti-α-defensin 5 (sc-53997, Santa Cruz Biotechnology, Inc,Dallas, Tex.) and rabbit anti-lysozyme (ab-2408) were used at a 1:50dilution in OP Quanto antibody Diluent (Thermo Fisher, Waltham, Wash.).Prior to addition of antibody for 45 minutes, tissues were incubated for10 min with Utravision hydrogen peroxide block (Thermo Fisher) followedby a 5 min incubation with Ultravisoion Quanto protein block. A singleincubation with Permanent Red was used for ileum tissue, whereas twoconsecutive 10 min permanent Red incubations were performed for colonictissue. Following hematoxylin counter staining, tissue was exposed toRichard-Allen Scientific Blueing Reagent (Thermo Fisher).

Antigen retrieval was performed in 1 mM EDTA pH 8.4, 0.05% Tween 20 for20 minutes at 98° C. (60° C. preheat/70° C. cool down) using theLabvision PT Module (Thermo Scioentific). Image color deconvolution wasperformed with Fiji ImageJ 1.51f (http://imagej.nih.gov/ij) using theFast Red, Fast Blue and DAB built in stain vector plugin.

Results

Nearly 30% of Indeterminate Colitis Patients Cannot be Delineated intoUC or CC

A retrospective investigation was conducted to identify a cohort ofpatients diagnosed with IC to determine if they could be properlydelineated into UC or CC over time. We followed 21 patients who werediagnosed with IC between the years 2000-2007 and reevaluated in 2014. Amean surveillance follow-up period was 8.7±3.7 (range, 4-14) years.Fifteen of the 21 (71.4%) had their original diagnosis changed; 9 to UC(43%) and 6 to CC (28.5%). Six (28.5%) patients remained clinicallyinconclusive and retained their diagnosis of IC (FIG. 1A). These datawere collected in the absence of any type of biomarker.

Thirty Percent of Restorative Proctocolectomy Operated Crohn's ColitisPatients were Misdiagnosed as Ulcerative Colitis

A retrospective investigation was conducted to identify a cohort ofpatients that underwent RPC and IPAA surgery for a definitive UCdiagnosis to determine if they had been misdiagnosed. We identified 67such patients. A mean surveillance follow-up period was 9.4 (range,6-13) years. A change in diagnosis to de novo Crohn's disease of theileal pouch was clinically observed in 20 (30%) patients (FIG. 1B). Inthe other 47 (70%) cases, the initial diagnosis of UC remainedclinically unchanged. These data were collected in the absence of anytype of biomarker. Because of these results, we sought to determine ifthere are potential genes that may be used to better differentiatebetween UC and CC at first clinical biopsy and prior to any surgicalintervention.

There is Differential Expression of Human α-Defensin-5 in InflammatoryBowel Disease

We initially performed whole-transcriptome microarray with RNA extractedand pooled from human full thickness colon samples from UC and CCpatients (n=5) using the Affymetrix gene expression array according tothe manufacturer's instructions (Affymetrix, Santa Clara, Calif.)Tissues from diverticulitis (DV) were used as control. This analysisshowed a total of 484 genes that were upor down-regulated (˜2-fold)between the two diseases. Among the upregulated genes were α-defensin-5,other antimicrobial peptides, and mucins (Table 1). HD5 was increasedthe most: 31-fold in CC vs. UC (in a previous study HD5 increase by118-fold in CC versus UC—data not shown). A full list of the microarrayresults can be found in Table 1.

To replicate these data in a different platform, an independent analysisby PCR array (NanoString Technologies Inc. Seattle, Wash.) was carriedout on 5 different human full thickness colon samples from UC and CCpatients. Although the NanoString array only specifically targetedinflammatory genes, the only gene to show up in both the microarray andthe PCR array was HD5. The NanoString array determined that HD5 wasincreased 118-fold in CC vs. UC in these human samples, compared to31-fold in the previous samples analyzed by microarray (Table 2).

To further validate these data, we assessed the expression of HD5 bysemi-quantitative RT-PCR using RNA extracted from moderate CC andmoderate UC tissues (n=3). This analysis also showed a significantincrease in transcript levels of HD5 in CC compared to UC (FIG. 2A, SEM,p<0.05). Several commercially available HD5 antibodies have beendeveloped. Due to the sequence homology of the alpha defensin class ofproteins, we tested a set of antibodies to assess specificity to HD5. Weperformed dot blots using commercially available antibodies againstrecombinant HD1-6. We determined that the monoclonal antibody from SantaCruz Biotechnology, Inc. (Santa Cruz, Calif.) showed the highest levelof specificity for HD5, and was therefore used in subsequent assays(FIG. 13). Next, we assessed the expression of HD5 by Western blotting(n=10 for each disease state). Samples were run individually on westernblots, with a combination of disease states on each blot, and we show anexample of an individual sample per disease state in a representativeblot (FIG. 2B). When we take each individual sample into considerationacross all western blots, protein densitometry analysis also showssignificantly higher levels of HD5 in moderate and severe CC compared toall other disease states (FIG. 2C, p<0.0001). Finally, we examined theexpression of HD5 in moderate disease activity of IBD and controltissues by IHC using FFPE sections. This analysis revealed that HD5levels are indeed increased in CC (FIG. 2G) when compared to DV, and UCand normal (NL) control tissue (FIGS. 2D, 2E and 2F). Quantification ofthe HD5 IHC staining spot counts by NEARAS revealed a 5.6-fold increaseof HD5 in CC vs. UC (FIG. 2H, p<0.0001). We believe the IHC dataexplains the weak western blot banding patterns. Because the westernblots were run with full-thickness samples, there is a low overallabundance of HD5 in the tissue; the IHC shows that it is much localizedin the base of individual colonic crypts. Because of this, furtheranalysis is done using IHC instead of western blots.

Table 1 shows a list of targets from an affymetrix cDNA microarray. Atotal of 484 genes were highlighted in the microarray as potentialmarkers for distinguishing UC from CC. The gene showing the largest foldchange between the two diseases was Human Defensin 5 (HD5).

Table 2 shows a full list of targets from NanoString Human InflammationPCR array. 16 inflammatory genes were changed in this subset of samples.HD5 was the only gene to appear in both the microarray and theNanoString PCR array.

TABLE 2 NanoString NanoString Microarray Gene p-value Fold Change FoldChange Symbol (CC vs UC) (CC vs UC) (CC vs UC) DEFA5 0.00182525 118.14531.0374 RBP2 0.282548 6.8909 — CD53 0.417119 −1.32516 — SAA2 0.575901−1.36908 — SNORD13P2 0.0839705 −1.42879 — SMAD4 0.00233383 −1.49572 —SNORD28 0.00995582 −1.58122 — ALOX5AP 0.153036 −1.61452 — SCARNA80.132287 −1.63997 — SNORD13 0.00409278 −1.87394 — UNQ2550 0.0386757−1.97314 — CLEC4D 0.168864 −2.03025 — STAP1 0.211401 −2.03524 — CYP4F3LP0.0584598 −2.37697 — SAA1 0.0988763 −2.42023 — IL6 0.167391 −4.90534 —

Human α-Defensin-5 Levels are Aberrant in Indeterminate Colitis andRestorative Proctocolectomy Operated Patients

In order to determine if HD5 could be used to assess whether IC patientscould be delineated into a diagnosis of either UC or CC, we assessedlevels of HD5 in surgical pathology colectomy samples via IHC inpatients described in FIG. 1A. In each instance of a final diagnosis ofCC, HD5 high NEARAS counts were in agreement with that diagnosis. Wealso found that when the 6 patients with unchanged IC diagnoses wereanalyzed via HD5 IHC NEARAS profile tests, 3 showed high HD5 count andagreed with the final diagnosis of CC, and 3 showed low HD5 count andwere in agreement with the final diagnosis of UC (Table 4, as shown inFIG. 13). Table 4 shows that IHC staining for HD5 agrees with finaldiagnostic outcome in a sample of IC patients even when there was noagreement with the attending physician.

Further, RPC and IPAA-operated patients described in FIG. 1B who had aclinical change in diagnosis to de novo Crohn's (n=20) and those whosediagnoses did not change (n=47) were also analyzed molecularly for HD5levels via NEARAS IHC counts. The patients whose diagnosis remainedunchanged showed only trace levels of HD5 (FIG. 8A). Patients whosediagnoses clinically changed from UC to de novo Crohn's showed prominentHD5 staining (FIG. 8B).

These images can be compared to normal ileum control (FIG. 8C).Differential quantification of HD5 levels by NEARAS counts for UC RPCand IPAA-operated patients who did not have their original diagnoseschanged vs. those with de novo Crohn's (FIG. 8A vs. 3B) werestatistically significant (p<0.0001) (FIG. 8D). In addition, statisticalanalysis to determine positive predictive values (PPVs) of HD5 inpatient tissue are 95.8% for CC and only 76.9% for UC. Chi squaredanalysis shows significant relatedness between high levels of HD5 and adiagnosis of CC (p<0.0001). These data indicate that HD5 could bedeveloped into a diagnostic tool to better distinguish CC from UC.

Aberrantly Regulated Human α-Defensin-5 in Crohn's Colitis Patients Maybe Caused by Ectopic Colonic Crypt Paneth Cells HD5 is a Paneth cellproduct; therefore, we wanted to determine if Paneth cells were presentin the colon crypt of Crohn's colitis patients. All 20 UC RPC operatedpatients with de novo Crohn's showed pools of ectopic crypt PCs in thecolectomy samples, as demonstrated by H&E representativephotomicrography (FIG. 9E). This was validated by IHC labeling of PCsusing lysozyme by microscopy, which confirmed the abundant presence ofPCs in CC colonic crypts (FIG. 9H, arrow). To validate whether the poolof HD5 expressed in CC and in de novo Crohn's colectomy samples wasindeed coming from colonic epithelial crypt PCs, we usedimmunohistochemically detection of PC markers α-Defensin 5 (DEFA5) andlysozyme (LYZ) and double staining IHC to colocalize PCs and HD5 oncolectomy samples. Lysozyme alone detects PCs. We demonstrate thepresence of abundant crypt PCs in CC colectomy patients (FIG. 9H)compared to all other colonic conditions analyzed (UC, DV, DVL and NL).Further, double staining analyses from de novo Crohn's (FIGS. 10A and5D), normal colon (FIG. 10J) and normal-ileum/control (FIG. 10G) arepresented. Image deconvolutions are displayed vertically to evaluatelysozyme-specific permanent red (FIGS. 10B, 5E and 5H) and HD5-specificDAB (FIGS. 10C, 5F and 5I). The normal colon image (FIG. 10J), whichlacks PCs, was not further processed. The results reconcile andrepresent a consensus among treating physicians.

Human α-Defensin-5 (DEFA5) is a Better Candidate Biomarker than PanethCells for Crohn's Colitis.

Finally, we sought to determine if HD5 and Paneth cells were bothupregulated in the normal, adjacent tissue of CC patients compared to UCpatients (FIG. 11). Immunohistochemistry for HD5 shows positive stainingin the base of the crypts in both inflamed and normal, adjacent tissueof CC patient samples (FIG. 11A). We were even able to see some positiveHD5 staining when the crypt structure is abolished due to excessiveinflammation and tissue damage (FIG. 11A, patient WD-12919, arrows).Unsurprisingly, in UC tissue, we saw either very low levels of HD5 or noexpression at all (FIG. 11B). We were very surprised, however, to findthat we could not see any Paneth cells in either the inflamed or normaladjacent tissues of any of the CC or UC patients surveyed (CC, n=3; UC,n=2) (FIGS. 11C and 6D). These results are surprising, considering ourearlier experiments surveying Paneth cells in a larger number ofpatients (FIG. 9). Because we can detect HD5 in the normal, adjacenttissue more readily than visualize Paneth cells, we believe that HD5will serve as a better candidate biomarker than Paneth cells for CC.

Studies of MMP-7

Semi-quantitative real-time PCR (qPCR) was used to measure transcriptlevels of MMP-7. To do this, RNA was extracted from three human colonbiopsy samples per condition; three each from moderate UC and CC, andfrom DV biopsy samples as a non-IBD control using the Qiagen RNeasyMiniprep Kit, (Valencia, Calif.). cDNA was generated using the iScriptcDNA synthesis kit (Bio-Rad, Hercules, Calif.), then used in the qPCRreactions using pre-designed TaqMan probes for MMP-7, and GAPHD control,and universal PCR master mix (Thermo Fisher Scientific, Waltham, Mass.).The reactions were run in triplicate using a CFX96 real-time PCRthermocycler (Bio-Rad). Data were analyzed according to the ΔΔCt method.

To assess any differences in the expression of HD5 and MMP-7 at theprotein level, colon surgical resections (n=10) were used from mild,moderate, and severe UC; mild, moderate, and severe CC; and non-IBD DVcontrol. Whole tissue protein extracts were prepared from full-thicknesscolon samples (n=10) using T-PER protein extraction kit according tomanufacturer's protocol (Thermo Fisher Scientific). Bradford Assays(Bio-Rad) were used to determine protein concentration, and equalamounts of protein were separated in 4-20% SDS-PAGE tris/glycine gel(sodium dodecyl sulphate-polyacrylamide gel electrophoresis) (Bio-Rad),then transferred to PVDF (polyvinylidene difluoride) membranes(Bio-Rad). The membranes were probed with antibodies against HD5, MMP-7,and β-actin loading control according to manufacturer's protocol. Blotswere visualized with Opti-4CN colorimetric detection kit (Bio-Rad) andimaged with ChemiDoc XRS+imaging system (Bio-Rad). Band intensities weremeasured and data analysis performed with Image Lab Software (Bio-Rad).

FIG. 3 is a bar graph of a qRT-PCR result showing a decrease in MMP-7levels in moderate CC compared to moderate UC, the inverse of HD5 levels(p<0.001). Western blot data for all disease states (n 10) shows adecrease in MMP-7 levels in CC compared to UC, significant when moderateand severe CC is compared to mild UC. FIG. 4 is a representative westernblot of MMP-7 in subjects having IBD. Expression of HD5 in IBD tissueswas examined by IHC using FFPE thin sections. MMP-7 levels (top) appearto decrease progressing from left to right. β-actin loading control isshown on bottom. FIG. 5 is a graphical representation of MMP-7 levelsshown in FIG. 3. Band intensities were measured and normalized toβ-actin loading control. Moderate and severe CC are statisticallysignificant when compared to mild UC (p<0.05 and p<0.005, respectively).FIGS. 8A-G are graphical representations showing MMP-7 and HD5 levelsare inversely expressed in IBD. Patient samples were matched and levelsof HD5 and MMP-7 were compared. In all disease states, MMP-7 and HD5levels are inversely expressed, and all differences are statisticallysignificant. As MMP-7 levels decrease, HD5 levels increase.

Discussion

Colectomy surgical pathology samples of patients with unambiguous CC andUC undergoing colectomy in connection with RPC and IPAA were analyzed[6,7]. We those protein profiles which had the necessary (i)specificity; (ii) sensitivity; (iii) discriminatory; and (iv) predictivecapacity to determine the heterogeneity of IBD [6,7] were identified andcompared. It was possible to molecularly delineate UC and CC withmolecular signatures of HD5 using IHC and quantified by NEARAS.Alpha-Defensins HD5 and HD6 are PC products and their altered expressionhas been linked to IBD pathogenesis.

It was not expected that one could not visualize PCs in these tissueseven though one could detect HD5 in the same tissue (FIG. 2H),especially compared to earlier experiments showing high levels of PCs inall CC patients surveyed (FIG. 2C). Whether the PCs are essential forstem cell maintenance in vivo remains debatable [27].

To date, there is no diagnostic gold standard tool for IBD.Differentiating UC and CC among patients with IC has remainedpainstaking and is a major challenge in endoscopic medicine andcolorectal surgery [1,12,28,29]. Clinicians use an inexactclassification system of clinical, endoscopy, radiologic, andhistopathology findings in order to diagnose CC and UC [21,30,31]. Evenwith a combination of these diagnostic modalities, up to 15% of IBDpatients are labeled as IC when no definitive evaluations can be made[13,30,32]. In addition, CC is mistakenly diagnosed and RPC andIPAA-operated as definitive UC in another 15% of IBD patients because ofoverlap in the clinical, endoscopic, radiological and histologicfindings [12,33-36]. Further, most IC patients who undergo RPC and IPAAsurgery for presumed UC are subsequently found to develop a recurrent denovo Crohn's disease in the ileal pouch [1,12,33]. This is a seriousconsequence that may hinder the restoration of intestinal continuity andits intractable nature leads to pouch failure, often requiring pouchdiversion or excision with a permanent terminal-ileostomy, resulting innegative psycho-sociological implications and poorer quality of life[1,29,31,36-41]. Curative treatment for UC is often surgical [42].

Success of RPC and IPAA surgery is largely dependent on careful patientselection combined with meticulous surgical technique and diagnosticaccuracy [9-11,13]. Available clinical presentations and experiencesuggest that it is difficult to identify patients with CC who are likelyto have a successful outcome after RPC and IPAA surgery [10,13,34,43].However, in highly selected patients with CC, RPC and IPAA has beenindicated [44-47]. Thus, RPC operation may be considered and shouldremain a careful option for certain subgroup of patients with CC, but anacceptable care option for patients with UC and for those IC patientspredicted to develop UC [9,42].

These studies of HD5 as a candidate biomarker for CC suggest it could bea diagnostic signature to efficiently distinguish CC from UC. Newlypublished data shows that patients with small bowel Crohn's disease(Crohn's ileitis) are characterized with a deficiency of HD5, as shownby a reduced expression and secretion of the Paneth cell HD5, afundamental feature of Crohn's ileitis [48-51]. Based on this study, inCC, the reverse is true. It was found that Paneth cell HD5 is apredominantly expressed antimicrobial peptide. This indicates thatdefinitive CC and Crohn's ileitis may have distinct etiologies andmechanisms. In these studies, all IC patient samples have beenreconciled into UC and CC using molecular biomarker, HD5, and verifiedthe reconciliation by patient outcomes (FIGS. 1 and 13 (Table 4)).

Accurately distinguishing CC from UC is of utmost importance whendetermining the candidacy of a patient for RPC [1,42]. Early diagnosticaccuracy of IBD will lead to timely appropriate medical options. Thisstudy confirms that HD5 can differentiate CC and UC and reclassify ICinto CC. In addition to distinguishing the colitides, HD5 couldobjectively be used to evaluate biophysiological processes andtherapeutic outcomes and potentially play a pivotal role in IBD clinicsas an attractive, non-invasive avenue [52,53].

Thus, this working example shows that tissue samples taken from patientssuffering from CD have levels of HD5 significantly higher than the HD5levels in samples from patients suffering from UC. Additionally, thisworking example shows that samples taken from patients suffering from CDhave levels of MMP-7 significantly lower than the MMP-7 levels insamples of patients suffering from UC.

REFERENCES

The following references were cited in the above working example. Suchcitation is not to be construed as an admission that any reference meetsthe legal definition of “prior art” in any country, nor as an admissionthat any reference is relevant to the patentability of anything claimed.Any such reference shall be incorporated herein by reference only to theextent it is necessary for a person of ordinary skill in the art to makeand use anything claimed.

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EXEMPLARY EMBODIMENTS

In addition to anything described above or currently claimed, it isspecifically contemplated that any of the following embodiments may beclaimed:

Emb. 1: A method of measuring HD5 in a patient suffering from or at riskof inflammatory bowel disease (IBD), said method comprising: obtaining asample from the patient; and measuring at least one of the expression ofHD5 and the concentration of HD5 in the sample.Emb. 2: A method of treating a patient suffering from or at risk ofinflammatory bowel disease (IBD), said method comprising: performing themethod of measuring HD5 in the patient according to embodiment 1; andperforming an intervention on the patient to treat Crohn's disease.Emb. 3: Any one of the methods of embodiments 1-2, comprising: comparingthe expression of HD5 or the concentration of HD5 in the sample to abenchmark value that is typical of a subject not suffering from Crohn'sdisease;and diagnosing Crohn's disease if the expression of HD5 or theconcentration of HD5 in the sample significantly exceeds the benchmarkvalue.Emb. 4: Any one of the methods of embodiments 1-3, wherein theexpression of HD5 or the concentration of HD5 in the sample exceeds abenchmark value that is typical of a subject not suffering from Crohn'sdisease.Emb. 5: Any one of the methods of embodiments 1-4, wherein theexpression of HD5 is measured to be significantly greater in the samplethan in a control sample from a subject not suffering from Crohn'sdisease.Emb. 6: Any one of the methods of embodiments 1-5, wherein theexpression of HD5 is measured to be at least about 31 times greater inthe sample than in a control sample from a subject not suffering fromCrohn's disease.Emb. 7: Any one of the methods of embodiments 1-6, wherein theexpression of HD5 is measured to be at least about 118 times greater inthe sample than in a control sample from a subject not suffering fromCrohn's disease.Emb. 8: Any one of the methods of embodiments 1-7, wherein theexpression of HD5 is measured to be greater than about 106 HD5 mRNAtranscripts per 10 ng RNA.Emb. 9: Any one of the methods of embodiments 1-8, wherein theexpression of HD5 is measured to be greater than 107 HD5 mRNAtranscripts per 10 ng RNA.Emb. 10: Any one of the methods of embodiments 1-9, wherein theexpression of HD5 is measured to be greater than 1.9×107 HD5 mRNAtranscripts per 10 ng RNA.Emb. 11: Any one of the methods of embodiments 1-10, wherein theexpression of HD5 is measured to be greater than 7×107 HD5 mRNAtranscripts per 10 ng RNA.Emb. 12: Any one of the methods of embodiments 1-11, wherein theexpression of HD5 is measured by qRT-PCR, wherein the method comprisesmeasuring the expression of HD5 mRNA in a control sample from a subjectnot suffering from Crohn's disease, and wherein the expression of HD5mRNA in the sample is significantly greater than the expression of HD5mRNA in the control sample.Emb. 13: Any one of the methods of embodiments 1-12, wherein the sampleis intestinal tissue, and comprising measuring the concentration of HD5by: immunostaining the sample with an anti-HD5 immunostaining agent; andmeasuring the percentage of cells in the sample that stain positive;wherein the percentage of cells in the sample that stain positive is atleast 10%.Emb. 14: Any one of the methods of embodiments 1-13, wherein the sampleis intestinal tissue, and comprising measuring the concentration of HD5by: immunostaining the sample with an anti-HD5 immunostaining agent; andmeasuring the percentage of cells in the sample that stain positive;wherein the percentage of cells in the sample that stain positive is atleast 20%.Emb. 15: Any one of the methods of embodiments 1-14, wherein the sampleis intestinal tissue, and comprising measuring the concentration of HD5by: immunostaining the sample with an anti-HD5 immunostaining agent; andmeasuring the percentage of cells in the sample that stain positive;wherein the percentage of cells in the sample that stain positive is atleast about 30%.Emb. 16: Any one of the methods of embodiments 1-15, wherein theintervention is not effective to treat ulcerative colitis.Emb. 17: Any one of the methods of embodiments 1-16, wherein theintervention is a surgery.Emb. 18: Any one of the methods of embodiments 1-17, wherein theintervention is a surgery selected from the group consisting of: ostomy,colostomy, ileostomy, bowel resection, colectomy, proctocolectomy, andstrictureplasty.Emb. 19: Any one of the methods of embodiments 1-18, wherein theintervention is administration of a drug.Emb. 20: Any one of the methods of embodiments 1-19, wherein theintervention is administration of a drug, to the exclusion of a surgery.Emb. 21: Any one of the methods of embodiments 1-20, wherein theintervention is administration of a drug selected from the groupconsisting of: a vitamin supplement, vitamin B12, vitamin D, a mineralsupplement, calcium, an anti-inflammatory, a corticosteroid, a5-aminosalicylate, an immunosuppressant, azathioprine, mercaptopurine,an anti-TNF-alpha antibody, infliximab, adalimumab, certolizumab pegol,methotrexate, an anti-α4-integrin antibody, natalizumab, vedolizumab, ananti-interleukin antibody, ustekinumab, an antibacterial antibiotic,ciprofloxacin, and metronidazole.Emb. 22: Any one of the methods of embodiments 1-21, wherein theintervention is administration of a drug selected from the groupconsisting of: certolizumab pegol, methotrexate, and natalizumab.Emb. 23: Any one of the methods of embodiments 1-22, wherein theintervention is placement of the subject on a low fat diet.Emb. 24: A method of treating a patient suffering from or at risk ofinflammatory bowel disease (IBD), said method comprising:performing the method of measuring HD5 in the patient according toembodiment 1; and; andperforming an intervention on the patient to treat ulcerative colitis.Emb. 25: The method of embodiment 24, comprising: comparing theexpression of HD5 or the concentration of HD5 in the sample to abenchmark value that is typical of a subject not suffering from Crohn'sdisease; and diagnosing ulcerative colitis if the expression of HD5 orthe concentration of HD5 in the sample does not significantly exceed thebenchmark value.Emb. 26: The method of any one of embodiments 24-25, wherein theexpression of HD5 or the concentration of HD5 in the sample is below abenchmark value that is typical of a subject suffering from Crohn'sdisease.Emb. 27: The method of any one of embodiments 24-25, wherein theexpression or concentration of HD5 in the sample is measured to besignificantly less than in a control sample from a subject sufferingfrom Crohn's disease.Emb. 28: The method of any one of embodiments 24-27, wherein theexpression of HD5 is measured in the sample is no more than about 1/31of expression of HD5 measured in a control sample from a subject notsuffering from Crohn's disease.Emb. 29: The method of any one of embodiments 24-28, wherein theexpression of HD5 is measured in the sample is no more than about 1/118of expression of HD5 measured in a control sample from a subject notsuffering from Crohn's disease.Emb. 30: The method of any one of embodiments 24-29, wherein theexpression of HD5 is measured to be less than 106 HD5 mRNA transcriptsper 10 ng RNA.Emb. 31: The method of any one of embodiments 24-30, wherein theexpression of HD5 is measured to be less than 107 HD5 mRNA transcriptsper 10 ng RNA.Emb. 32: The method of any one of embodiments 24-31, wherein theexpression of HD5 is measured to be less than 1.9×107 HD5 mRNAtranscripts per 10 ng RNA.Emb. 33: The method of any one of embodiments 24-32, wherein theexpression of HD5 is measured to be less than 6×105 HD5 mRNA transcriptsper 10 ng RNA.Emb. 34: The method of any one of embodiments 24-33, wherein theexpression of HD5 is measured by qRT-PCR, wherein the method comprisesmeasuring the expression of HD5 in a control sample from a subjectsuffering from Crohn's disease, and wherein the expression of HD5 mRNAin the sample is significantly less than the expression of HD5 in thecontrol sample.Emb. 35: The method of any one of embodiments 24-34, wherein the sampleis intestinal tissue, and comprising measuring the concentration of HD5by: immunostaining the sample with an anti-HD5 immunostaining agent; andmeasuring the percentage of cells in the sample that stain positive;wherein the percentage of cells in the sample that stain positive isless than 10%.Emb. 36: The method of any one of embodiments 24-35, wherein the sampleis intestinal tissue, and comprising measuring the concentration of HD5by: immunostaining the sample with an anti-HD5 immunostaining agent; andmeasuring the percentage of cells in the sample that stain positive;wherein the percentage of cells in the sample that stain positive isless than 20%.Emb. 37: The method of any one of embodiments 24-36, wherein the sampleis intestinal tissue, and comprising measuring the concentration of HD5by: immunostaining the sample with an anti-HD5 immunostaining agent; andmeasuring the percentage of cells in the sample that stain positive;wherein the percentage of cells in the sample that stain positive isless than about 30%.Emb. 38: The method of any one of embodiments 24-37, wherein theintervention is not effective to treat Crohn's disease.Emb. 39: The method of any one of embodiments 24-38, wherein theintervention is a surgery.Emb. 40: The method of any one of embodiments 24-39, wherein theintervention is a surgery combined with the administration of a drug.Emb. 41: The method of any one of embodiments 24-40, wherein theintervention is a surgery selected from the group consisting of: aproctocolectomy, and an ileal pouch anal anastomosis.Emb. 42: The method of any one of embodiments 24-41, wherein theintervention is administration of a drug selected from the groupconsisting of: an iron supplement, an anti-inflammatory, acorticosteroid, a 5-aminosalicylate, an immunosuppressant, azathioprine,mercaptopurine, cyclosporine, an anti-TNF-alpha antibody, infliximab,adalimumab, golimumab, methotrexate, an anti-α4-integrin antibody,vedolizumab, an antibacterial antibiotic, ciprofloxacin, andmetronidazole.Emb. 43: The method of any one of embodiments 24-42, wherein theintervention is administration of a drug selected from the groupconsisting of: cyclosporine, and golimumab.Emb. 44: The method of any one of embodiments 1-43, wherein theexpression of HD5 is measured.Emb. 45: The method of any one of embodiments 1-44, wherein theconcentration of HD5 is measured.Emb. 46: The method of any one of embodiments 1-45, wherein the sampleis intestinal tissue.Emb. 47: The method of any one of embodiments 1-46, wherein the sampleis from the subject's large intestine.Emb. 48: The method of any one of embodiments 1-47, wherein the sampleis colonic tissue.Emb. 49: The method of any one of embodiments 1-48, wherein the sampleis ileal tissue.Emb. 50: The method of any one of embodiments 1-49, wherein theexpression of HD5 or the concentration of HD5 is measured in the sampleex vivo.Emb. 51: The method of any one of embodiments 1-50, wherein HD5expression is measured by a technique selected from the group consistingof: whole transcriptome analysis, whole-transcriptome microarray,Northern blot, DNA microarray, PCR, sequencing PCR, RT-PCR, quantitativePCR, restriction fragment length polymorphism, in situ hybridizationassay, and a competitive-binding assay.Emb. 52: The method of any one of embodiments 1-51, wherein HD5concentration is measured by a technique selected from the groupconsisting of: Western blot, ELISA, two-dimensional gel electrophoresis,mass spectrometry, protein interaction profiling, a competitive bindingassay, a non-competitive binding assay, a radioimmunoassay, an enzymeimmunoassays, an enzyme linked immunosorbent assay (ELISA), a sandwichimmunoassay, a precipitation reaction, a gel diffusion reaction, animmunodiffusion assay, an agglutination assay, a complement-fixationassay, an immunoradiometric assay, a fluorescent immunoassay, a proteinA immunoassay, NMR analysis, and an immunoelectrophoresis assay.Emb. 53: The method of any one of embodiments 1-52, wherein the patientis suffering from IBD.Emb. 54: The method of any one of embodiments 1-53, wherein the patientdisplays a symptom selected from the group consisting of: severediarrhea, abdominal pain, fatigue, and weight loss.Emb. 55: The method of any one of embodiments 1-54, wherein the patientdisplays severe diarrhea, abdominal pain, fatigue, and weight loss.Emb. 56: The method of any one of embodiments 1-55, wherein theexpression of HD5 is measured.Emb. 57: The method of any one of embodiments 1-56, wherein theconcentration of HD5 is measured.Emb. 58: The method of any one of embodiments 1-57, further comprisingmeasuring at least one of the expression of MMP-7 and the concentrationof MMP-7 in the sample.Emb. 59: A method of measuring MMP-7 in a patient suffering from or atrisk of inflammatory bowel disease (IBD), said method comprising:obtaining a sample from the patient; and measuring at least one of theexpression of MMP-7 and the concentration of MMP-7 in the sample.Emb. 60: A method of treating a patient suffering from or at risk ofinflammatory bowel disease (IBD), said method comprising:performing the method of measuring MMP-7 in the patient according to anyone of embodiments 58-59; andperforming an intervention on the patient to treat Crohn's disease.Emb. 61: The method of any one of embodiments 58-60, comprising:comparing the expression of MMP-7 or the concentration of MMP-7 in thesample to a benchmark value that is typical of a subject not sufferingfrom ulcerative colitis; and diagnosing Crohn's disease if theexpression of MMP-7 or the concentration of MMP-7 in the sample does notsignificantly exceed the benchmark value.Emb. 62: The method of any one of embodiments 58-61, wherein theexpression of MMP-7 or the concentration of MMP-7 in the sample is belowa benchmark value that is typical of a subject suffering from ulcerativecolitis.Emb. 63: The method of any one of embodiments 58-61, wherein theexpression of MMP-7 is measured to be significantly less in the samplethan in a control sample from a subject suffering from ulcerativecolitis.Emb. 64: The method of any one of embodiments 58-63, wherein theexpression of MMP-7 is measured in the sample to be at most about 1/10of the expression of MMP-7 measured in a control sample from a subjectnot suffering from ulcerative colitis.Emb. 65: The method of any one of embodiments 58-64, wherein theexpression of MMP-7 is measured by qRT-PCR, wherein the method comprisesmeasuring the expression of MMP-7 in a control sample from a subjectsuffering from ulcerative colitis, and wherein the expression of MMP-7in the sample is significantly less than the expression of MMP-7 in thecontrol sample.Emb. 66: The method of any one of embodiments 58-65, wherein the sampleis intestinal tissue, and comprising measuring the concentration ofMMP-7 by: immunostaining the sample with an antiMMP-7 immunostainingagent; and measuring the percentage of cells in the sample that stainpositive.Emb. 67: The method of any one of embodiments 58-66, wherein theintervention is not effective to treat ulcerative colitis.Emb. 68: The method of any one of embodiments 58-67, wherein theintervention is a surgery.Emb. 69: The method of any one of embodiments 58-68, wherein theintervention is a surgery selected from the group consisting of: ostomy,colostomy, ileostomy, bowel resection, colectomy, proctocolectomy, andstrictureplasty.Emb. 70: The method of any one of embodiments 58-69, wherein theintervention is administration of a drug.Emb. 71: The method of any one of embodiments 58-70, wherein theintervention is administration of a drug, to the exclusion of a surgery.Emb. 72: The method of any one of embodiments 58-71, wherein theintervention is administration of a drug selected from the groupconsisting of: a vitamin supplement, vitamin B12, vitamin D, a mineralsupplement, calcium, an anti-inflammatory, a corticosteroid, a5-aminosalicylate, an immunosuppressant, azathioprine, mercaptopurine,an anti-TNF-alpha antibody, infliximab, adalimumab, certolizumab pegol,methotrexate, an anti-α4-integrin antibody, natalizumab, vedolizumab, ananti-interleukin antibody, ustekinumab, an antibacterial antibiotic,ciprofloxacin, and metronidazole.Emb. 73: The method of any one of embodiments 58-72, wherein theintervention is administration of a drug selected from the groupconsisting of: certolizumab pegol, methotrexate, and natalizumab.Emb. 74: The method of any one of embodiments 58-73, wherein theintervention is placement of the subject on a low fat diet.Emb. 75: A method of treating a patient suffering from or at risk ofinflammatory bowel disease (IBD), said method comprising:performing the method of measuring MMP-7 in the patient according toembodiment 58; andperforming an intervention on the patient to treat ulcerative colitis.Emb. 76: The method of any one of embodiments 58, 59 and 75, comprising:comparing the expression of MMP-7 or the concentration of MMP-7 in thesample to a benchmark value that is typical of a subject not sufferingfrom ulcerative colitis; and diagnosing ulcerative colitis if theexpression of MMP-7 or the concentration of MMP-7 in the samplesignificantly exceeds the benchmark value.Emb. 77: The method of any one of embodiments 58, 59 and 75-76, whereinthe expression of MMP-7 or the concentration of MMP-7 in the sample isabove a benchmark value that is typical of a subject not suffering fromulcerative colitis.Emb. 78: The method of any one of embodiments 58, 59 and 75-76, whereinthe expression or concentration of MMP-7 in the sample is measured to besignificantly greater than in a control sample from a subject notsuffering from ulcerative colitis.Emb. 79: The method of any one of embodiments 58, 59 and 75-78, whereinthe expression of MMP-7 measured in the sample is at least about 5 timesthe expression of MMP-7 measured in a control sample from a subject notsuffering from ulcerative colitis.Emb. 80: The method of any one of embodiments 58, 59 and 75-79, whereinthe expression of MMP-7 measured in the sample is at least about 10times the expression of MMP-7 measured in a control sample from asubject not suffering from ulcerative colitis.Emb. 81: The method of any one of embodiments 58, 59 and 75-80, whereinthe expression of MMP-7 is measured by qRT-PCR, wherein the methodcomprises measuring the expression of MMP-7 in a control sample from asubject not suffering from ulcerative colitis, and wherein theexpression of MMP-7 in the sample is significantly greater than theexpression of MMP-7 in the control sample.Emb. 82: The method of any one of embodiments 58, 59 and 75-81, whereinthe sample is intestinal tissue, and comprising measuring theconcentration of MMP-7 by: immunostaining the sample with an antiMMP-7immunostaining agent; and measuring the percentage of cells in thesample that stain positive.Emb. 83: The method of any one of embodiments 58, 59 and 75-82, whereinthe intervention is not effective to treat Crohn's disease.Emb. 84: The method of any one of embodiments 58, 59 and 75-83, whereinthe intervention is a surgery.Emb. 85: The method of any one of embodiments 58, 59 and 75-84, whereinthe intervention is a surgery combined with the administration of adrug.Emb. 86: The method of any one of embodiments 58, 59 and 75-85, whereinthe intervention is a surgery selected from the group consisting of: aproctocolectomy, and an ileal pouch anal anastomosis.Emb. 87: The method of any one of embodiments 58, 59 and 75-86, whereinthe intervention is administration of a drug selected from the groupconsisting of: an iron supplement, an anti-inflammatory, acorticosteroid, a 5-aminosalicylate, an immunosuppressant, azathioprine,mercaptopurine, cyclosporine, an anti-TNF-alpha antibody, infliximab,adalimumab, golimumab, methotrexate, an anti-α4-integrin antibody,vedolizumab, an antibacterial antibiotic, ciprofloxacin, andmetronidazole.Emb. 88: The method of any one of embodiments 58, 59 and 75-87, whereinthe intervention is administration of a drug selected from the groupconsisting of: cyclosporine, and golimumab.Emb. 89: The method of any one of embodiments 58-88, wherein theexpression of MMP-7 or the concentration of MMP-7 is measured in thesample ex vivo.Emb. 90: The method of any one of embodiments 58-89, wherein MMP-7expression is measured by a technique selected from the group consistingof: whole transcriptome analysis, whole-transcriptome microarray,Northern blot, DNA microarray, PCR, sequencing PCR, RT-PCR, quantitativePCR, restriction fragment length polymorphism, in situ hybridizationassay, and a competitive-binding assay.Emb. 91: The method of any one of embodiments 58-90, wherein MMP-7concentration is measured by a technique selected from the groupconsisting of: Western blot, ELISA, two-dimensional gel electrophoresis,mass spectrometry, protein interaction profiling, a competitive bindingassay, a non-competitive binding assay, a radioimmunoassay, an enzymeimmunoassays, an enzyme linked immunosorbent assay (ELISA), a sandwichimmunoassay, a precipitation reaction, a gel diffusion reaction, animmunodiffusion assay, an agglutination assay, a complement-fixationassay, an immunoradiometric assay, a fluorescent immunoassay, a proteinA immunoassay, NMR analysis, and an immunoelectrophoresis assay.Emb. 92: The method of any one of embodiments 58-91, wherein the patientis suffering from IBD.Emb. 93: The method of any one of embodiments 58-92, wherein the patientdisplays a symptom selected from the group consisting of: severediarrhea, abdominal pain, fatigue, and weight loss.Emb. 94: The method of any one of embodiments 58-93, wherein the patientdisplays severe diarrhea, abdominal pain, fatigue, and weight loss.Emb. 95: The method of any one of embodiments 58-94, wherein the sampleis intestinal tissue.Emb. 96: The method of any one of embodiments 58-95, wherein the sampleis from the subject's large intestine.Emb. 97: The method of any one of embodiments 58-96, wherein the sampleis colonic tissue.Emb. 98: The method of any one of embodiments 58-97, wherein the sampleis ileal tissue.Emb. 99: A kit for measuring HD5 and MMP-7 in a sample, the kitcomprising: a first assay for measuring at least one of the expressionof human HD5 and the concentration of human HD5 in a sample; and asecond assay for measuring at least one of the expression of human MMP-7and the concentration of human MMP-7 in a sample.Emb. 100: The kit of embodiment 99, wherein said kit is for thediagnosis of inflammatory bowel disease.Emb. 101: The kit of any one of embodiments 99-100, wherein the firstassay comprises an antibody that recognizes human HD5; and wherein thesecond assay comprises antibody that recognizes human MMP-7.Emb. 102: The kit of any one of embodiments 99-101, wherein the firstassay comprises an oligonucleotide probe that binds to human HD5 cDNA;and wherein the second assay comprises an oligonucleotide probe thatbinds to human MMP-7 cDNA.Emb. 103: The kit of any one of embodiments 99-102, wherein the firstassay comprises a pair of primers complementary to a region of human HD5cDNA; and wherein the second assay comprises a pair of primerscomplementary to a region of human MMP-7 cDNA.Emb. 104: The kit of any one of embodiments 99-103, wherein: the firstassay comprises a means for detecting HD5 protein; and the second assaycomprises a means for detecting MMP-7 protein.Emb. 105: The kit of embodiment 104, wherein: the means for detectingthe HD5 protein is a first probe comprising a first ligand group thatspecifically binds to HD5 protein; and the means for detecting MMP-7protein is a second probe comprising a second ligand group thatspecifically binds to MMP-7 protein.Emb. 106: The kit of embodiment 105, wherein the first ligand group isan immunoglobulin.Emb. 107: The kit of any one of embodiments 105-106, wherein the secondligand group is an immunoglobulin.Emb. 108: The kit of any one of embodiments 105-107, wherein the firstprobe and the second probe are immobilized to a surface.Emb. 109: The kit of any one of embodiments 99-108, wherein: the assayfor measuring the expression of HD5 detects a first target sequence ofat least 15 bp that is present in a first cDNA or mRNA of HD5; and theassay for measuring the expression of MMP-7 detects a second targetsequence of at least 15 bp that is present in a second cDNA or mRNA ofMMP-7.Emb. 110: The kit of embodiment 109, wherein: the assay for detectingthe first target sequence comprises a first probe comprising a firstpolynucleotide of at least 15 bp that hybridizes under highly stringentconditions with the first target sequence of at least 15 bp that ispresent in the first cDNA or mRNA of HD5; and the assay for detectingthe second target sequence comprises a second probe comprising a secondpolynucleotide of at least 15 bp that hybridizes under highly stringentconditions with the second target sequence of at least 15 bp that ispresent in the second cDNA or mRNA of MMP-7.Emb. 111: The kit of any one of embodiments 109-110, comprising acontainer of a reverse transcriptase.Emb. 112: The kit of any one of embodiments 102-111, wherein the firstprobe comprises a first reporter, and the second probe comprises asecond reporter.Emb. 113: The kit of embodiment 112, wherein the first reporter isselected from the group consisting of: a radionuclide, a stable isotope,a fluorophore, a chromophore, an enzyme, a magnetic particle, and aquantum dot; and the second reporter selected from the group consistingof: a radionuclide, a fluorophore, a chromophore, an enzyme, a magneticparticle, and a quantum dot.Emb. 114: The kit of any one of embodiments 110-113, wherein the firstpolynucleotide is single stranded DNA; and wherein the secondpolynucleotide is single stranded DNA.Emb. 115: The kit of any one of embodiments 102-114, wherein the firstprobe and the second probe are components of a DNA array.Emb. 116: The kit of any one of embodiments 102-115, wherein the firstprobe and the second probe are components of a DNA microarray.Emb. 117: The kit of any one of embodiments 110-116, wherein the firstpolynucleotide is at least 20 bp and the second polynucleotide is atleast 20 bp.Emb. 118: The kit of any one of embodiments 110-117, wherein the firstpolynucleotide is at least 25 bp and the second polynucleotide is atleast 25 bp.Emb. 119: A method of diagnosing and treating Crohn's disease in asubject suffering from inflammatory bowel disease, the methodcomprising:obtaining a sample from the patient;measuring at least one of the expression of HD5 and the concentration ofHD5 in the sample;comparing the expression of HD5 or the concentration of HD5 in thesample to a benchmark value that is typical of a subject not sufferingfrom Crohn's disease;diagnosing Crohn's disease if the expression of HD5 or the concentrationof HD5 in the sample significantly exceeds the benchmark value; andtreating the subject for Crohn's disease by way of a non-surgicalintervention.Emb. 120: A method of diagnosing Crohn's disease in a subject sufferingfrom inflammatory bowel disease, comprising: measuring the level of HD5or HD5 expression in a sample from the subject, wherein the measuring isselected from the group consisting of radioimmunoassays, reversetranscriptase PCR (RT-PCR) assays, immunohistochemistry assays, in situhybridization assays, competitive-binding assays, Western Blot analyses,ELISA assays and proteomic approaches, cation-ion exchange, NMRanalysis, genome-wide transcriptome analysis, mass spectrometry, andcombinations thereof; and diagnosing the subject as suffering fromCrohn's disease if the level of HD5 is indicative of a subject havingCrohn's disease.Emb. 121: The method of embodiment 120, wherein the subject is diagnosedas suffering from Crohn's disease if the level of HD5 or HD5 expressionis from about 1.9×10⁷ HD5 mRNA Transcript per 10 ng RNA to about 7×10⁷HD5 mRNA Transcript per 10 ng RNA.Emb. 122: A method of diagnosing ulcerative colitis in a subjectsuffering from inflammatory bowel disease, comprising: measuring thelevel of HD5 or HD5 expression in a sample from the subject, wherein themeasuring is selected from the group consisting of radioimmunoassays,reverse transcriptase PCR (RT-PCR) assays, immunohistochemistry assays,in situ hybridization assays, competitive-binding assays, Western Blotanalyses, ELISA assays and proteomic approaches, cation-ion exchange,NMR analysis, genome-wide transcriptome analysis, mass spectrometry, andcombinations thereof; and diagnosing the subject as suffering fromulcerative colitis if the level of HD5 or HD5 expression is indicativeof a subject having ulcerative colitis.Emb. 123: The method of embodiment 122, wherein the subject is diagnosedas suffering from ulcerative colitis if the level of HD5 or HD5expression is from about 6×10⁵ HD5 mRNA Transcript per 10 ng RNA toabout 1.8×10⁷ HD5 mRNA Transcript per 10 ng RNA.Emb. 124: A method of treating inflammatory bowel disease in a subject,comprising: measuring the level of HD5 or HD5 expression present in asample obtained from the subject, said measuring step wherein themeasuring is selected from the group consisting of radioimmunoassays,reverse transcriptase PCR (RT-PCR) assays, immunohistochemistry assays,in situ hybridization assays, competitive-binding assays, Western Blotanalyses, ELISA assays and proteomic approaches, cation-ion exchange,NMR analysis, genome-wide transcriptome analysis, mass spectrometry, andcombinations thereof, whereby a level of HD5 or HD5 expression isobtained; and if the level of HD5 or HD5 expression is at a levelindicative of a subject not having Crohn's disease, treating theinflammatory bowel disease in the subject with a suitable medicaltreatment for ulcerative colitis; if the level of HD5 or HD5 expressionis at a level indicative of a subject having Crohn's disease, treatingthe inflammatory bowel disease in the subject with a suitable medicaltreatment for Crohn's disease.Emb. 125: The method according to embodiment 122, wherein the suitablemedical treatment for ulcerative colitis comprises performing ilealpouch anal anastomosis in the subject.Emb. 126: The method according to embodiment 122, wherein the suitablemedical treatment for Crohn's disease comprises the administration ofone or more of 5aminosalicylate, a corticosteroid, and animmunosuppressant to the subject.Emb. 127: The method according to embodiment 122, wherein the sample iscollected from the large intestine, and the subject is human.Emb. 128: An assay for detecting elevated levels of HD5, comprising anHD5 antibody capable of binding with HD5.Emb. 129: The assay according to embodiment 128, wherein the assay isprovided in a kit.Emb. 130: The novel and non-obvious embodiments and features disclosedherein.Emb. 131: A method of measuring a biomarker in a patient suffering fromor at risk of inflammatory bowel disease (IBD), said method comprising:obtaining a sample from the patient; and measuring a level of thebiomarker in the same, the level of the biomarker selected from thegroup consisting of: the expression of the biomarker, the activity ofthe biomarker, and the concentration of the biomarker; wherein saidbiomarker is selected from Table 1.Emb. 132: A method of treating a patient suffering from or at risk ofinflammatory bowel disease (IBD), said method comprising: performing themethod of measuring the level of the biomarker in the patient accordingto embodiment 131; and performing an intervention on the patient totreat Crohn's disease.Emb. 133: Any one of the methods of embodiments 131-132, comprising:comparing the level of the biomarker in the sample to a benchmark valuethat is typical of a subject not suffering from Crohn's disease; anddiagnosing Crohn's disease if the expression of the biomarker in thesample significantly differs from the benchmark value.

CONCLUSIONS

It is to be understood that any given elements of the disclosedembodiments of the invention may be embodied in a single structure, asingle step, a single substance, or the like. Similarly, a given elementof the disclosed embodiment may be embodied in multiple structures,steps, substances, or the like.

The foregoing description illustrates and describes the processes,machines, manufactures, compositions of matter, and other teachings ofthe present disclosure. Additionally, the disclosure shows and describesonly certain embodiments of the processes, machines, manufactures,compositions of matter, and other teachings disclosed, but as mentionedabove, it is to be understood that the teachings of the presentdisclosure are capable of use in various other combinations,modifications and environments and are capable of changes ormodifications within the scope of the teachings as expressed herein,commensurate with the skill and/or knowledge of a person having ordinaryskill in the relevant art. The embodiments described hereinabove arefurther intended to explain certain best modes known of practicing theprocesses, machines, manufactures, compositions of matter, and otherteachings of the present disclosure and to enable others skilled in theart to utilize the teachings of the present disclosure in such, orother, embodiments and with the various modifications required by theparticular applications or uses. Accordingly, the processes, machines,manufactures, compositions of matter, and other teachings of the presentdisclosure are not intended to limit the exact embodiments and examplesdisclosed herein. Any section headings herein are provided only forconsistency with the suggestions of 37 C.F.R. § 1.77, or otherwise toprovide organizational queues. These headings shall not limit orcharacterize the invention(s) set forth herein.

TABLE 1 Gene Gene p-value Fold Information Symbol RefSeq (CC vs UC)Increase NM_021010 // DEFA5 // defensin, alpha 5, DEFA5 NM_0210107.23E−05 31.0374 Paneth cell-specific // 8p23.1 // 1670 NM_002909 //REG1A // regenerating islet- REG1A NM_002909 0.00321456 21.9439 derived1 alpha // 2p12 // 5967 /// ENS NM_138938 // REG3A // regeneratingislet- REG3A NM_138938 0.000310891 17.3268 derived 3 alpha // 2p12 //5068 /// NM_ NM_001926 // DEFA6 // defensin, alpha 6, DEFA6 NM_0019260.0024893 16.139 Paneth cell-specific // 8p23.1 // 1671 NM_058186 //FAM3B // family with FAM3B NM_058186 0.00116588 14.6887 sequencesimilarity 3, member B // 21q22.3 // NM_006507 // REG1B // regeneratingislet- REG1B NM_006507 0.0120953 13.9675 derived 1 beta // 2p12 // 5968/// ENST NM_001074 // UGT2B7 // UDP UGT2B7 NM_001074 0.0154146 9.92532glucuronosyltransferase 2 family, polypeptide B7 // 4 NM_001285 // CLCA1// chloride channel CLCA1 NM_001285 0.00297816 9.07579 accessory 1 //1p22.3 // 1179 /// ENST000 NM_003122 // SPINK1 // serine peptidaseSPINK1 NM_003122 0.007176 7.60063 inhibitor, Kazal type 1 // 5q32 //6690 NM_001076 // UGT2B15 // UDP UGT2B15 NM_001076 0.0169187 7.12294glucuronosyltransferase 2 family, polypeptide B15 // NM_001076 //UGT2B15 // UDP UGT2B15 NM_001076 0.0169187 7.12294glucuronosyltransferase 2 family, polypeptide B15 // NM_000343 // SLC5A1// solute carrier SLC5A1 NM_000343 0.00447091 7.0494 family 5(sodium/glucose cotransporter), m NM_000134 // FABP2 // fatty acidbinding FABP2 NM_000134 0.0300574 6.63756 protein 2, intestinal //4q28-q31 // 21 NM_000035 // ALDOB // aldolase B, ALDOB NM_0000350.0444145 6.30502 fructose-bisphosphate // 9q21.3-q22.2 // 229/NM_002770 // PRSS2 // protease, serine, 2 PRSS2 NM_002770 0.00526656.27999 (trypsin 2) // 7q34 // 5645 /// ENST00 NM_005379 // MYO1A //myosin IA // MYO1A NM_005379 0.00588172 5.72861 12q13-q14 // 4640 ///ENST00000300119 // MYO1 NM_007329 // DMBT1 // deleted in DMBT1 NM_0073290.0365636 5.56609 malignant brain tumors 1 // 10q26.13 // 1755 //NM_031457 // MS4A8B // membrane-spanning MS4A8B NM_031457 0.005779525.34254 4-domains, subfamily A, member 8B // 11 NM_001041 // SI //sucrase-isomaltase SI NM_001041 0.0417578 5.23854 (alpha-glucosidase) //3q25.2-q26.2 // 647 NM_000482 // APOA4 // apolipoprotein A-IV // APOA4NM_000482 0.0468523 5.15957 11q23 // 337 /// ENST00000357780 //NM_006418 // OLFM4 // olfactomedin 4 // OLFM4 NM_006418 0.038931 5.0588313q14.3 // 10562 /// ENST00000219022 // NM_000482 // APOA4 //apolipoprotein A-IV // APOA4 NM_000482 0.0472178 4.92519 11q23 // 337/// ENST00000357780 // NM_004133 // HNF4G // hepatocyte nuclear HNF4GNM_004133 0.0113549 4.8964 factor 4, gamma // 8q21.11 // 3174 ///NM_017675 // CDHR2 // cadherin-related CDHR2 NM_017675 0.002535684.82206 family member 2 // 5q35.2 // 54825 /// NM NM_005588 // MEP1A //meprin A, alpha MEP1A NM_005588 0.0198087 4.78504 (PABA peptidehydrolase) // 6p12-p11 // 42 NM_002354 // EPCAM // epithelial cell EPCAMNM_002354 0.0242383 4.77321 adhesion molecule // 2p21 // 4072 /// ENSTNM_001172312 // PLS1 // plastin 1 // 3q23 // PLS1 NM_001172312 0.01552484.73894 5357 /// NM_001145319 // PLS1 // pl NM_002354 // EPCAM //epithelial cell EPCAM NM_002354 0.0297878 4.72533 adhesion molecule //2p21 // 4072 /// ENST NM_001150 // ANPEP // alanyl (membrane) ANPEPNM_001150 0.0203087 4.58929 aminopeptidase // 15q25-q26 // 290 /// ENM_001077 // UGT2B17 // UDP UGT2B17 NM_001077 0.0267812 4.51157glucuronosyltransferase 2 family, polypeptide B17 // NM_002591 // PCK1// PCK1 NM_002591 0.0333639 4.50793 phosphoenolpyruvate carboxykinase 1(soluble) // 20q13.31 / NM_021804 // ACE2 // angiotensin I ACE2NM_021804 0.0271919 4.49025 converting enzyme (peptidyl-dipeptidase A) 2NM_024308 // DHRS11 // dehydrogenase/ DHRS11 NM_024308 0.0176773 4.41914reductase (SDR family) member 11 // 17q12/ NM_019010 // KRT20 // keratin20 // KRT20 NM_019010 0.026162 4.35459 17q21.2 // 54474 ///ENST00000167588 // KRT2 ENST00000319509 // MUC3A // mucin 3A, MUC3AENST00000319509 0.00353785 4.28484 cell surface associated // 7q22 //4584 // NM_000379 // XDH // xanthine XDH NM_000379 0.00289109 4.17476dehydrogenase // 2p23.1 // 7498 /// ENST00000379416 NM_007127 // VIL1 //villin 1 // 2q35 // 7429 /// VIL1 NM_007127 0.00825691 4.16925ENST00000248444 // VIL1 // vil NM_025130 // HKDC1 // hexokinase domainHKDC1 NM_025130 0.00344261 4.13874 containing 1 // 10q22.1 // 80201 ///ENS NR_029578 // MIR192 // microRNA 192 // MIR192 NR_029578 0.001998844.12467 11q13.1 // 406967 NM_004063 // CDH17 // cadherin 17, LI CDH17NM_004063 0.0331015 4.12001 cadherin (liver-intestine) // 8q22.1 // 10NM_024922 // CES3 // carboxylesterase 3 // CES3 NM_024922 0.00223544.11886 16q22.1 // 23491 ///NM_001185177 // NM_033049 // MUC13 // mucin13, cell MUC13 NM_033049 0.0271079 4.11287 surface associated // 3q21.2// 56667 /// E NM_000888 // ITGB6 // integrin, beta 6 // ITGB6 NM_0008880.000602949 4.09738 2q24.2 // 3694 /// ENST00000283249 // NM_004963 //GUCY2C // guanylate GUCY2C NM_004963 0.00645462 4.0793 cyclase 2C (heatstable enterotoxin receptor)/ NM_004293 // GDA // guanine deaminase //GDA NM_004293 0.0208862 4.0739 9q21.13 // 9615 /// ENST00000358399 //NM_001307 // CLDN7 // claudin 7 // 17p13 // CLDN7 NM_001307 0.02134044.06183 1366 /// NM_001185022 // CLDN7 // cl NR_033807 // CYP3A5 //cytochrome P450, CYP3A5 NR_033807 0.0046334 4.04376 family 3, subfamilyA, polypeptide 5 // NM_021924 // CDHR5 // cadherin-related CDHR5NM_021924 0.00480695 3.97925 family member 5 // 11p15.5 // 53841 /// NNM_001010922 // BCL2L15 // BCL2-like 15 // BCL2L15 NM_001010922 0.0270533.96946 1p13.2 // 440603 /// ENST00000393316 NM_020770 // CGN //cingulin // 1q21 // CGN NM_020770 0.00129584 3.94184 57530 ///ENST00000271636 // CGN // cing NM_032787 // GPR128 // G protein-coupledGPR128 NM_032787 0.00779494 3.93937 receptor 128 // 3q12.2 // 84873 ///ENS NM_138933 // A1CF // APOBEC1 A1CF NM_138933 0.00976589 3.79699complementation factor // 10q11.23 // 29974 /// NM_ NM_152311 // CLRN3// clarin 3 // 10q26.2 // CLRN3 NM_152311 0.0132404 3.74982 119467 ///ENST00000368671 // CLRN3 NM_007072 // HHLA2 // HERV-H LTR- HHLA2NM_007072 0.0139075 3.74668 associating 2 // 3q13.13 // 11148 ///ENST00000 NM_003399 // XPNPEP2 // X-prolyl XPNPEP2 NM_003399 0.03593483.73179 aminopeptidase (aminopeptidase P) 2, membrane-b NM_021258 //IL22RA1 // interleukin 22 IL22RA1 NM_021258 0.00520995 3.72759 receptor,alpha 1 // 1p36.11 // 58985 /// NM_000149 // FUT3 // fucosyltransferase3 FUT3 NM_000149 0.0106419 3.70158 (galactoside3(4)-L-fucosyltransferase NM_002644 // PIGR // polymeric PIGR NM_0026440.0363588 3.68869 immunoglobulin receptor // 1q31-q41 // 5284 /// ENM_001136503 // C19orf77 // chromosome C19orf77 NM_001136503 0.01148673.6586 19 open reading frame 77 // 19p13.3 // 28 NR_024626 // C17orf73// chromosome 17 C17orf73 NR_024626 0.00240775 3.64138 open readingframe 73 // 17q21.33 // 5501 NM_020973 // GBA3 // glucosidase, beta,GBA3 NM_020973 0.0362758 3.63402 acid 3 (cytosolic) // 4p15.2 // 57733// NM_023944 // CYP4F12 // cytochrome CYP4F12 NM_023944 0.004688273.62246 P450, family 4, subfamily F, polypeptide 12/ NM_024320 // PRR15L// proline rich 15-like // PRR15L NM_024320 0.0331566 3.60367 17q21.32// 79170 /// ENST0000030 NM_005495 // SLC17A4 // solute carrier SLC17A4NM_005495 0.0299201 3.59753 family 17 (sodium phosphate), member 4 //NM_001135099 // TMPRSS2 // transmembrane TMPRSS2 NM_001135099 0.03512573.57585 protease, serine 2 // 21q22.3 // 7113/ NM_001193434 // C10orf81// chromosome C10orf81 NM_001193434 0.00228381 3.5687 10 open readingframe 81 // 10q25.3 // 79 NM_001935 // DPP4 // dipeptidyl-peptidase DPP4NM_001935 0.0302652 3.49144 4 // 2q24.3 // 1803 /// ENST0000036053NM_001644 // APOBEC1 // apolipoprotein B APOBEC1 NM_001644 0.01380083.48792 mRNA editing enzyme, catalytic polypept NM_004360 // CDH1 //cadherin 1, type 1, CDH1 NM_004360 0.010781 3.48059 E-cadherin(epithelial) // 16q22.1 // 9 NM_024921 // POF1B // premature ovarianPOF1B NM_024921 0.0313161 3.44457 failure, 1B // Xq21.2 // 79983 ///ENST0 NM_002416 // CXCL9 // chemokine (C-X-C CXCL9 NM_002416 0.002487343.44146 motif) ligand 9 // 4q21 // 4283 /// ENST0 NM_014479 // ADAMDEC1// ADAM-like, ADAMDEC1 NM_014479 0.00203661 3.42469 decysin 1 // 8p21.2// 27299 /// NM_00114527 NM_001112706 // SCIN // scinderin // SCINNM_001112706 0.00493508 3.3952 7p21.3 // 85477 /// NM_033128 // SCIN //sc NR_024345 // NCRNA00262 // non-protein NCRNA00262 NR_024345 0.0374733.39502 coding RNA 262 // 12q24.31 // 283460 NM_002273 // KRT8 //keratin 8 // 12q13 // KRT8 NM_002273 0.0146545 3.39222 3856 ///ENST00000293308 // KRT8 // k NM_001038603 // MARVELD2 // MARVEL MARVELD2NM_001038603 0.0179974 3.37682 domain containing 2 // 5q13.2 // 153562/// E NM_001038603 // MARVELD2 // MARVEL MARVELD2 NM_001038603 0.01799743.37682 domain containing 2 // 5q13.2 // 153562 /// E NM_144575 //CAPN13 // calpain 13 // CAPN13 NM_144575 0.013239 3.36885 2p22-p21 //92291 /// ENST00000295055 // CA NM_022129 // PBLD // phenazine PBLDNM_022129 0.00497915 3.3666 biosynthesis-like protein domain containing// 10 NM_000775 // CYP2J2 // cytochrome P450, CYP2J2 NM_000775 0.01960933.36302 family 2, subfamily J, polypeptide 2 // NM_001135195 // SLC39A5// solute carrier SLC39A5 NM_001135195 0.00623473 3.34227 family 39(metal ion transporter), mem NM_138788 // TMEM45B // transmembraneTMEM45B NM_138788 0.0306305 3.33725 protein 45B // 11q24.3 // 120224 ///ENST0 NM_176813 // AGR3 // anterior gradient AGR3 NM_176813 0.04008233.32266 homolog 3 (Xenopus laevis) // 7p21.1 // 1 NM_022901 // LRRC19 //leucine rich repeat LRRC19 NM_022901 0.0294679 3.31296 containing 19 //9p21.2 // 64922 /// NM_139053 // EPS8L3 // EPS8-like 3 // EPS8L3NM_139053 0.00371579 3.29224 1p13.3 // 79574 /// NM_133181 // EPS8L3 //NM_017697 // ESRP1 // epithelial splicing ESRP1 NM_017697 0.02346653.27492 regulatory protein 1 // 8q22.1 // 5484 NM_002457 // MUC2 //mucin 2, oligomeric MUC2 NM_002457 0.0182535 3.26416 mucus/gel-forming// 11p15.5 // 4583 // NR_001296 // TRY6 // trypsinogen C // 7q34 // TRY6NR_001296 0.0203767 3.24356 154754 /// NM_002770 // PRSS2 // p NM_002773// PRSS8 // protease, serine, 8 // PRSS8 NM_002773 0.0131026 3.240516p11.2 // 5652 /// ENST00000317508 NM_025214 // CCDC68 // coiled-coildomain CCDC68 NM_025214 0.00627753 3.2264 containing 68 // 18q21 //80323 /// NM NM_001943 // DSG2 // desmoglein 2 // DSG2 NM_0019430.0357587 3.22627 18q12.1 // 1829 /// ENST00000261590 // DSG2 NM_000772// CYP2C18 // cytochrome CYP2C18 NM_000772 0.0100284 3.20876 P450,family 2, subfamily C, polypeptide 18/ NM_000767 // CYP2B6 // cytochromeP450, CYP2B6 NM_000767 0.00589423 3.19484 family 2, subfamily B,polypeptide 6 // NM_016234 // ACSL5 // acyl-CoA synthetase ACSL5NM_016234 0.00353915 3.19242 long-chain family member 5 // 10q25.1-NM_145865 // ANKS4B // ankyrin repeat ANKS4B NM_145865 0.027168 3.16823and sterile alpha motif domain containing NM_032579 // RETNLB //resistin like beta // RETNLB NM_032579 0.0226491 3.14305 3q13.1 // 84666/// ENST00000295755 NM_021978 // ST14 // suppression of ST14 NM_0219780.0143682 3.14171 tumorigenicity 14 (colon carcinoma) // 11q24 NM_000492// CFTR // cystic fibrosis CFTR NM_000492 0.0330127 3.13524transmembrane conductance regulator (ATP-bi NM_018842 // BAIAP2L1 //BAI1-associated BAIAP2L1 NM_018842 0.00626097 3.13099 protein 2-like 1// 7q22.1 // 55971 /// NM_001165958 // GSDMB // gasdermin B // GSDMBNM_001165958 0.0013942 3.1309 17q12 // 55876 /// NM_001042471 // GSDMBNM_024422 // DSC2 // desmocollin 2 // DSC2 NM_024422 0.0115939 3.1186218q12.1 // 1824 /// NM_004949 // DSC2 // d NM_006017 // PROM1 //prominin 1 // PROM1 NM_006017 0.0116042 3.10273 4p15.32 // 8842 ///NM_001145847 // PROM1 // NM_017878 // HRASLS2 // HRAS-like HRASLS2NM_017878 0.0267887 3.09847 suppressor 2 // 11q12.3 // 54979 ///ENST00000 NM_002203 // ITGA2 // integrin, alpha 2 ITGA2 NM_0022030.00793505 3.07141 (CD49B, alpha 2 subunit of VLA-2 recepto NM_005123 //NR1H4 // nuclear receptor NR1H4 NM_005123 0.0456782 3.06865 subfamily 1,group H, member 4 // 12q23.1 NM_001145862 // MTMR11 // myotubularinMTMR11 NM_001145862 0.00116554 3.03455 related protein 11 // 1q12-q21 //10903/ NM_018414 // ST6GALNAC1 // ST6 (alpha- ST6GALNAC1 NM_0184140.0240185 3.0202 N-acetyl-neuraminyl-2,3-beta-galactosyl-1, NM_001080527// MYO7B // myosin VIIB // MYO7B NM_001080527 0.00130692 2.99927 2q21.1// 4648 /// ENST00000428314 // MY NM_002153 // HSD17B2 // hydroxysteroidHSD17B2 NM_002153 0.0213389 2.99803 (17-beta) dehydrogenase 2 //16q24.1-q24. AK095678 // LOC151009 // hypothetical LOC151009 AK0956780.000466288 2.99502 LOC151009 // 2q13 // 151009 /// AK056084/ NM_000769// CYP2C19 // cytochrome CYP2C19 NM_000769 0.0193957 2.99186 P450,family 2, subfamily C, polypeptide 19/ NM_000790 // DDC // dopadecarboxylase DDC NM_000790 0.0257511 2.98778 (aromatic L-amino aciddecarboxylase) // NM_001143948 // C6orf105 // chromosome C6orf105NM_001143948 0.0220945 2.95786 6 open reading frame 105 // 6p24.1 // 848NM_001015001 // CKMT1A // creatine CKMT1A NM_001015001 0.042629 2.95709kinase, mitochondrial 1A // 15q15 // 548596/ NM_001015001 // CKMT1A //creatine CKMT1A NM_001015001 0.042629 2.95709 kinase, mitochondrial 1A// 15q15 // 548596/ NM_019893 // ASAH2 // N-acylsphingosine ASAH2NM_019893 0.0167497 2.95643 amidohydrolase (non-lysosomal ceramidaseNM_001002236 // SERPINA1 // serpin SERPINA1 NM_001002236 0.01709292.94245 peptidase inhibitor, clade A (alpha-1 antipro NM_002031 // FRK// fyn-related kinase // FRK NM_002031 0.0177896 2.93608 6q21-q22.3 //2444 /// ENST00000368626 NM_001190482 // PCSK5 // proprotein PCSK5NM_001190482 0.00160967 2.92603 convertase subtilisin/kexin type 5 //9q21.3 NM_004415 // DSP // desmoplakin // 6p24 // DSP NM_0044150.0116502 2.91732 1832 /// NM_001008844 // DSP // desmo NM_004591 //CCL20 // chemokine (C-C CCL20 NM_004591 0.0229351 2.91511 motif) ligand20 // 2q33-q37 // 6364 /// NM NM_000561 // GSTM1 // glutathione S- GSTM1NM_000561 0.032505 2.91233 transferase mu 1 // 1p13.3 // 2944 /// NM_14NM_000927 // ABCB1 // ATP-binding ABCB1 NM_000927 0.03279 2.89709cassette, sub-family B (MDR/TAP), member 1 // NM_000187 // HGD //homogentisate 1,2- HGD NM_000187 0.0180393 2.8961 dioxygenase // 3q13.33// 3081 /// ENST000 NM_000187 // HGD // homogentisate 1,2- HGD NM_0001870.0180393 2.8961 dioxygenase // 3q13.33 // 3081 /// ENST000 NM_153676 //USH1C // Usher syndrome USH1C NM_153676 0.00547469 2.88241 1C (autosomalrecessive, severe) // 11p14.3 NM_005624 // CCL25 // chemokine (C-C CCL25NM_005624 0.0492359 2.86049 motif) ligand 25 // 19p13.2 // 6370 /// ENSNM_004174 // SLC9A3 // solute carrier SLC9A3 NM_004174 0.0173616 2.8567family 9 (sodium/hydrogen exchanger), memb NM_001306 // CLDN3 // claudin3 // 7q11.23 // CLDN3 NM_001306 0.0490185 2.84657 1365 ///ENST00000395145 // CLDN3 NM_001114309 // ELF3 // E74-like factor 3 ELF3NM_001114309 0.00265363 2.84098 (ets domain transcription factor, epitNM_000507 // FBP1 // fructose-1,6- FBP1 NM_000507 0.022351 2.83767bisphosphatase 1 // 9q22.3 // 2203 /// NM_0011 NM_025257 // SLC44A4 //solute carrier SLC44A4 NM_025257 0.0415598 2.83697 family 44, member 4// 6p21.3 // 80736 // NM_025257 // SLC44A4 // solute carrier SLC44A4NM_025257 0.0415598 2.83697 family 44, member 4 // 6p21.3 // 80736 //NM_025257 // SLC44A4 // solute carrier SLC44A4 NM_025257 0.04155982.83697 family 44, member 4 // 6p21.3 // 80736 // NM_001017970 //TMEM30B // transmembrane TMEM30B NM_001017970 0.00717685 2.83259 protein30B // 14q23.1 // 161291 /// EN NM_003963 // TM4SF5 // transmembrane 4TM4SF5 NM_003963 0.0295851 2.82875 L six family member 5 // 17p13.3 //9032 NM_002242 // KCNJ13 // potassium KCNJ13 NM_002242 0.0400838 2.82471inwardly-rectifying channel, subfamily J, membe NM_017655 // GIPC2 //GIPC PDZ domain GIPC2 NM_017655 0.0155498 2.81938 containing family,member 2 // 1p31.1 // 5 NM_001127605 // LIPA // lipase A, LIPANM_001127605 0.000449938 2.81611 lysosomal acid, cholesterol esterase //10q23. NM_001249 // ENTPD5 // ectonucleoside ENTPD5 NM_001249 0.01186972.81265 triphosphate diphosphohydrolase 5 // 14q24 NM_005358 // LMO7 //LIM domain 7 // LMO7 NM_005358 0.00460576 2.80795 13q22.2 // 4008 ///NM_015842 // LMO7 // LI NM_018667 // SMPD3 // sphingomyelin SMPD3NM_018667 0.00228114 2.80665 phosphodiesterase 3, neutral membrane(neutr NM_004563 // PCK2 // phosphoenolpyruvate PCK2 NM_0045630.00983672 2.79262 carboxykinase 2 (mitochondrial) // 14q1 NM_003657 //BCAS1 // breast carcinoma BCAS1 NM_003657 0.0213345 2.78368 amplifiedsequence 1 // 20q13.2 // 8537/ NM_024850 // BTNL8 // butyrophilin-like 8// BTNL8 NM_024850 0.0446038 2.7769 5q35.3 // 79908 /// NM_001040462 //NM_020672 // S100A14 // S100 calcium S100A14 NM_020672 0.0202797 2.77156binding protein A14 // 1q21.3 // 57402 /// NM_033229 // TRIM15 //tripartite motif- TRIM15 NM_033229 0.0097609 2.77095 containing 15 //6p21.3 // 89870 /// ENS NM_033229 // TRIM15 // tripartite motif- TRIM15NM_033229 0.0097609 2.77095 containing 15 // 6p21.3 // 89870 /// ENSNM_033229 // TRIM15 // tripartite motif- TRIM15 NM_033229 0.00976092.77095 containing 15 // 6p21.3 // 89870 /// ENS NM_001144060 // NHSL1// NHS-like 1 // NHSL1 NM_001144060 0.0124428 2.7705 6q23.3 // 57224 ///NM_020464 // NHSL1 // NM_003869 // CES2 // carboxylesterase 2 // CES2NM_003869 0.0197746 2.76326 16q22.1 // 8824 /// NR_036684 // CES2NM_199187 // KRT18 // keratin 18 // 12q13 // KRT18 NM_199187 0.02729382.7567 3875 /// NM_000224 // KRT18 // kera NM_002842 // PTPRH // proteintyrosine PTPRH NM_002842 0.00126103 2.75623 phosphatase, receptor type,H // 19q13.4 NM_001105248 // TMC5 // transmembrane TMC5 NM_0011052480.015439 2.74553 channel-like 5 // 16p12.3 // 79838 /// NM_ NM_001145809// MYH14 // myosin, heavy MYH14 NM_001145809 0.00203315 2.74198 chain14, non-muscle // 19q13.33 // 79784 NM_001054 // SULT1A2 //sulfotransferase SULT1A2 NM_001054 0.0273843 2.73 family, cytosolic, 1A,phenol-preferrin NM_024850 // BTNL8 // butyrophilin-like 8 // BTNL8NM_024850 0.0433332 2.7165 5q35.3 // 79908 /// NM_001159708 // NM_006147// IRF6 // interferon regulatory IRF6 NM_006147 0.00663477 2.71435factor 6 // 1q32.3-q41 // 3664 /// EN NM_000457 // HNF4A // hepatocytenuclear HNF4A NM_000457 0.00414138 2.70616 factor 4, alpha // 20q13.12// 3172 /// NM_138809 // CMBL // CMBL NM_138809 0.0336993 2.69623carboxymethylenebutenolidase homolog (Pseudomonas) // 5p15. NM_001080467// MYO5B // myosin VB // MYO5B NM_001080467 0.00639465 2.69568 18q21 //4645 /// ENST00000285039 // MYO5B NM_153274 // BEST4 // bestrophin 4 //BEST4 NM_153274 0.0313639 2.68747 1p33-p32.3 // 266675 ///ENST00000372207/ NM_020775 // KIAA1324 // KIAA1324 // KIAA1324 NM_0207750.0214297 2.68133 1p13.3 // 57535 /// ENST00000234923 // KIAANM_001004320 // TMEM195 // transmembrane TMEM195 NM_001004320 0.01496662.67293 protein 195 // 7p21.2 // 392636 /// ENS NM_001091 // ABP1 //amiloride binding ABP1 NM_001091 0.0487109 2.66772 protein 1 (amineoxidase (copper-containi NM_016245 // HSD17B11 // hydroxysteroidHSD17B11 NM_016245 0.0216559 2.66473 (17-beta) dehydrogenase 11 //4q22.1 // NM_006144 // GZMA // granzyme A GZMA NM_006144 0.006182422.66284 (granzyme 1, cytotoxic T-lymphocyte- associated s NM_001039372// HEPACAM2 // HEPACAM family HEPACAM2 NM_001039372 0.0201907 2.6524member 2 // 7q21.3 // 253012 /// NM_1 NM_001197097 // PRSS3 // protease,PRSS3 NM_001197097 0.0173103 2.63924 serine, 3 // 9p11.2 // 5646 ///NM_007343 // NM_012214 // MGAT4A // mannosyl (alpha- MGAT4A NM_0122140.00113208 2.62742 1,3-)-glycoprotein beta-1,4-N-acetylgluco NM_019894// TMPRSS4 // transmembrane TMPRSS4 NM_019894 0.0362683 2.60764protease, serine 4 // 11q23.3 // 56649 /// NM_003810 // TNFSF10 // tumornecrosis TNFSF10 NM_003810 0.0129809 2.60509 factor (ligand)superfamily, member 10 // NM_022842 // CDCP1 // CUB domain CDCP1NM_022842 0.0167874 2.60268 containing protein 1 // 3p21.31 // 64866 ///NM NM_001136493 // MFSD2A // major MFSD2A NM_001136493 0.003436182.59815 facilitator superfamily domain containing 2A // NM_018265 //C1orf 106 // chromosome 1 C1orf106 NM_018265 0.00613223 2.59677 openreading frame 106 // 1q32.1 // 55765 NM_000063 // C2 // complementcomponent C2 NM_000063 0.0117239 2.59406 2 // 6p21.3 // 717 ///NM_001145903 // C NM_000063 // C2 // complement component C2 NM_0000630.0117239 2.59406 2 // 6p21.3 // 717 /// NM_001145903 // C NM_000625 //NOS2 // nitric oxide synthase NOS2 NM_000625 0.0089305 2.59304 2,inducible // 17q11.2-q12 // 4843/ NM_001677 // ATP1B1 // ATPase, Na+/K+ATP1B1 NM_001677 0.0131783 2.58871 transporting, beta 1 polypeptide //1q24/ NM_004751 // GCNT3 // glucosaminyl (N- GCNT3 NM_004751 0.04321972.58761 acetyl) transferase 3, mucin type // 15q21 NM_002021 // FMO1 //flavin containing FMO1 NM_002021 0.0408097 2.57646 monooxygenase 1 //1q24.3 // 2326 /// ENS NM_033292 // CASP1 // caspase 1, CASP1 NM_0332920.00634065 2.57013 apoptosis-related cysteine peptidase (interleukNM_147161 // ACOT11 // acyl-CoA ACOT11 NM_147161 0.0462671 2.53682thioesterase 11 // 1p32.3 // 26027 /// ENST00000 NM_001039112 // FER1L6// fer-1-like 6 FER1L6 NM_001039112 0.0413201 2.53444 (C. elegans) //8q24.1 // 654463 /// ENST NM_212543 // B4GALT4 // UDP- B4GALT4 NM_2125430.00083206 2.53146 Gal:betaGIcNAc beta 1,4- galactosyltransferase, polyNM_182762 // MACC1 // metastasis MACC1 NM_182762 0.0113734 2.52994associated in colon cancer 1 // 7p21.1 // 34638 NM_001461 // FMO5 //flavin containing FMO5 NM_001461 0.0227505 2.52925 monooxygenase 5 //1q21.1 // 2330 /// NM_ NM_031219 // HDHD3 // haloacid HDHD3 NM_0312190.00048055 2.52696 dehalogenase-like hydrolase domain containing 3/NM_001010872 // FAM83B // family with FAM83B NM_001010872 0.008062042.52496 sequence similarity 83, member B // 6p12.1 NM_024533 // CHST5 //carbohydrate (N- CHST5 NM_024533 0.026327 2.51739 acetylglucosamine 6-O)sulfotransferase 5 NM_000063 // C2 // complement component C2 NM_0000630.0114041 2.51419 2 // 6p21.3 // 717 /// NM_001145903 // C NM_004624 //VIPR1 // vasoactive intestinal VIPR1 NM_004624 0.00331244 2.50863peptide receptor 1 // 3p22 // 7433 / NM_004572 // PKP2 // plakophilin 2// 12p11 // PKP2 NM_004572 0.042448 2.49612 5318 /// NM_001005242 //PKP2 // NM_032521 // PARD6B // par-6 partitioning PARD6B NM_0325210.00395798 2.49598 defective 6 homolog beta (C. elegans) NM_024915 //GRHL2 // grainyhead-like 2 GRHL2 NM_024915 0.00624177 2.49455(Drosophila) // 8q22.3 // 79977 /// ENST NM_003982 // SLC7A7 // solutecarrier SLC7A7 NM_003982 0.00813405 2.49274 family 7 (cationic aminoacid transporter, NM_198584 // CA13 // carbonic anhydrase CA13 NM_1985840.00510852 2.48988 XIII // 8q21.2 // 377677 /// ENST0000032ENST00000319509 // MUC3A // mucin 3A, MUC3A ENST00000319509 0.01358832.4817 cell surface associated // 7q22 // 4584 // NM_021102 // SPINT2 //serine peptidase SPINT2 NM_021102 0.0219176 2.48131 inhibitor, Kunitztype, 2 // 19q13.1 // NM_080489 // SDCBP2 // syndecan binding SDCBP2NM_080489 0.000789754 2.47862 protein (syntenin) 2 // 20p13 // 27111/NM_001144967 // NEDD4L // neural NEDD4L NM_001144967 0.0227827 2.47791precursor cell expressed, developmentally down- NM_001982 // ERBB3 //v-erb-b2 ERBB3 NM_001982 0.0175723 2.47531 erythroblastic leukemia viraloncogene homolog 3 NM_000240 // MAOA // monoamine oxidase MAOA NM_0002400.0446884 2.47082 A // Xp11.3 // 4128 /// ENST00000338702/ NM_182960 //PRELID2 // PRELI domain PRELID2 NM_182960 0.00837834 2.47032 containing2 // 5q32 // 153768 /// NM_13849 NM_017720 // STAP2 // signaltransducing STAP2 NM_017720 0.016285 2.46781 adaptor family member 2 //19p13.3 // 5 NM_138700 // TRIM40 // tripartite motif- TRIM40 NM_1387000.0336507 2.45989 containing 40 // 6p22.1 // 135644 /// EN NM_000050 //ASS1 // argininosuccinate ASS1 NM_000050 0.0132614 2.43678 synthase 1 //9q34.1 // 445 /// NM_054012 NM_005021 // ENPP3 // ectonucleotide ENPP3NM_005021 0.0149678 2.43651 pyrophosphatase/phosphodiesterase 3 // 6q22NM_001130080 // IFI27 // interferon, alpha- IFI27 NM_001130080 0.01402362.43613 inducible protein 27 // 14q32 // 3429 NM_001979 // EPHX2 //epoxide hydrolase EPHX2 NM_001979 0.00690804 2.43531 2, cytoplasmic //8p21 // 2053 /// BC011 NM_017700 // ARHGEF38 // Rho guanine ARHGEF38NM_017700 0.00476968 2.42966 nucleotide exchange factor (GEF) 38 // 4q24NM_019080 // NDFIP2 // Nedd4 family NDFIP2 NM_019080 0.00576011 2.42832interacting protein 2 // 13q31.1 // 54602 // NM_001135181 // SLC5A9 //solute carrier SLC5A9 NM_001135181 0.0296431 2.42215 family 5(sodium/glucose cotransporter) NM_032717 // AGPAT9 // 1-acylglycerol-3-AGPAT9 NM_032717 0.0147877 2.41843 phosphate O-acyltransferase 9 //4q21.23 NM_001145303 // TMC4 // transmembrane TMC4 NM_0011453030.00110774 2.41442 channel-like 4 // 19q13.42 // 147798 /// N NM_138700// TRIM40 // tripartite motif- TRIM40 NM_138700 0.0250665 2.41358containing 40 // 6p22.1 // 135644 /// EN NM_138700 // TRIM40 //tripartite motif- TRIM40 NM_138700 0.0250665 2.41358 containing 40 //6p22.1 // 135644 /// EN NM_203463 // LASS6 // LAG1 homolog, LASS6NM_203463 0.00156196 2.41203 ceramide synthase 6 // 2q24.3 // 253782 ///NM_001730 // KLF5 // Kruppel-like factor 5 KLF5 NM_001730 0.01290152.40278 (intestinal) // 13q22.1 // 688 /// EN NM_001265 // CDX2 //caudal type CDX2 NM_001265 0.0471437 2.402 homeobox 2 // 13q12.3 // 1045/// ENST000003810 NM_000239 // LYZ // lysozyme // 12q15 // LYZ NM_0002390.0118582 2.39899 4069 /// ENST00000261267 // LYZ // lyso NM_022772 //EPS8L2 // EPS8-like 2 // EPS8L2 NM_022772 0.00191717 2.39231 11p15.5 //64787 /// ENST00000318562 // EP NM_025153 // ATP10B // ATPase, class V,ATP10B NM_025153 0.0273664 2.38677 type 10B // 5q34 // 23120 ///ENST000003 NM_178445 // CCRL1 // chemokine (C-C CCRL1 NM_1784450.0328488 2.38032 motif) receptor-like 1 // 3q22 // 51554 ///NM_001031803 // LLGL2 // lethal giant LLGL2 NM_001031803 0.003513952.36948 larvae homolog 2 (Drosophila) // 17q25.1/ NM_175058 // PLEKHA7// pleckstrin PLEKHA7 NM_175058 0.00170237 2.36502 homology domaincontaining, family A member 7 NM_006714 // SMPDL3A // sphingomyelinSMPDL3A NM_006714 0.0236138 2.36218 phosphodiesterase, acid-like 3A //6q22.31 NR_024158 // LOC25845 // hypothetical LOC25845 NR_0241580.0297858 2.35341 LOC25845 // 5p15.33 // 25845 /// ENST00000 NM_016339// RAPGEFL1 // Rap guanine RAPGEFL1 NM_016339 0.026897 2.3526 nucleotideexchange factor (GEF)-like 1 // NM_015888 // HOOK1 // hook homolog 1HOOK1 NM_015888 0.0336071 2.34842 (Drosophila) // 1p32.1 // 51361 ///ENST000 NM_138737 // HEPH // hephaestin // Xq11- HEPH NM_1387370.0118198 2.34595 q12 // 9843 /// NM_001130860 // HEPH // NM_012079 //DGAT1 // diacylglycerol O- DGAT1 NM_012079 0.023252 2.34522acyltransferase 1 // 8q24.3 // 8694 /// E NM_012079 // DGAT1 //diacylglycerol O- DGAT1 NM_012079 0.023252 2.34522 acyltransferase 1 //8q24.3 // 8694 /// E NM_001017535 // VDR // vitamin D (1,25- VDRNM_001017535 0.0115491 2.34153 dihydroxyvitamin D3) receptor // 12q13.1NM_001029874 // REP15 // RAB15 effector REP15 NM_001029874 0.04779632.33656 protein // 12p11.22 // 387849 /// ENST00 NM_198495 // CTAGE4 //CTAGE family, CTAGE4 NM_198495 0.00065154 2.33596 member 4 // 7q35 //100128553 /// NM_001145 NM_006548 // IGF2BP2 // insulin-like growthIGF2BP2 NM_006548 8.80E−05 2.33476 factor 2 mRNA binding protein 2 // 3NM_002985 // CCL5 // chemokine (C-C CCL5 NM_002985 0.0247261 2.33002motif) ligand 5 // 17q11.2-q12 // 6352 /// E NM_001005328 // OR2A7 //olfactory OR2A7 NM_001005328 0.00337105 2.32021 receptor, family 2,subfamily A, member 7 // NM_018284 // GBP3 // guanylate binding GBP3NM_018284 0.013933 2.31798 protein 3 // 1p22.2 // 2635 /// ENST00000NM_002829 // PTPN3 // protein tyrosine PTPN3 NM_002829 0.0212048 2.31511phosphatase, non-receptor type 3 // 9q31 NM_021073 // BMP5 // bonemorphogenetic BMP5 NM_021073 0.0201876 2.31001 protein 5 // 6p12.1 //653 /// ENST00000 NM_178176 // MOGAT3 // monoacylglycerol MOGAT3NM_178176 0.00641018 2.30988 O-acyltransferase 3 // 7q22.1 // 346606NM_000666 // ACY1 // aminoacylase 1 // ACY1 NM_000666 0.0261486 2.305813p21.1 // 95 /// L07548 // ACY1 // aminoa NM_001098634 // RBM47 // RNAbinding RBM47 NM_001098634 0.00857247 2.30203 motif protein 47 // 4p14// 54502 /// NM_01 NM_080658 // ACY3 // aspartoacylase ACY3 NM_0806580.0498753 2.301 (aminocyclase) 3 // 11q13.2 // 91703 /// ENS NR_003587// MYO15B // myosin XVB MYO15B NR_003587 0.00759021 2.29754 pseudogene// 17q25.1 // 80022 /// BC027875 // NM_005435 // ARHGEF5 // Rho guanineARHGEF5 NM_005435 0.00766916 2.29684 nucleotide exchange factor (GEF) 5// 7q33-q NM_005435 // ARHGEF5 // Rho guanine ARHGEF5 NM_0054350.00846455 2.29311 nucleotide exchange factor (GEF) 5 // 7q33-qNM_001017967 // MARVELD3 // MARVEL MARVELD3 NM_001017967 0.01241862.2921 domain containing 3 // 16q22.2 // 91862 /// N NM_003389 // CORO2A// coronin, actin CORO2A NM_003389 0.0203606 2.28709 binding protein, 2A// 9q22.3 // 7464 /// NM_031469 // SH3BGRL2 // SH3 domain SH3BGRL2NM_031469 0.0214373 2.27245 binding glutamic acid-rich protein like 2 //NM_030766 // BCL2L14 // BCL2-like 14 BCL2L14 NM_030766 0.0037691 2.26634(apoptosis facilitator) // 12p13-p12 // 793 NR_002713 // NPY6R //neuropeptide Y NPY6R NR_002713 0.0429642 2.26407 receptor Y6(pseudogene) // 5q31 // 4888 // NM_001114086 // CLIC5 // chloride CLIC5NM_001114086 0.0269601 2.25433 intracellular channel 5 // 6p12.3 //53405 /// NM_003645 // SLC27A2 // solute carrier SLC27A2 NM_0036450.040906 2.2539 family 27 (fatty acid transporter), membe NM_001136050// DHRS1 // DHRS1 NM_001136050 0.000608529 2.23931dehydrogenase/reductase (SDR family) member 1 // 14q12 NM_002164 // IDO1// indoleamine 2,3- IDO1 NM_002164 0.00532092 2.2314 dioxygenase 1 //8p12-p11 // 3620 /// ENST0 NM_001171192 // GDPD2 // GDPD2 NM_0011711920.0455387 2.23073 glycerophosphodiester phosphodiesterase domaincontaini NM_016445 // PLEK2 // pleckstrin 2 // PLEK2 NM_016445 0.01840482.22972 14q23.3 // 26499 /// ENST00000216446 // PL NR_033122 // PDZD3 //PDZ domain PDZD3 NR_033122 0.0104609 2.2269 containing 3 // 11q23.3 //79849 /// NM_0011684 NM_000932 // PLCB3 // phospholipase C, PLCB3NM_000932 0.01393 2.22018 beta 3 (phosphatidylinositol-specific) //NM_018235 // CNDP2 // CNDP dipeptidase CNDP2 NM_018235 0.0009581732.20566 2 (metallopeptidase M20 family) // 18q22. NM_032562 // PLA2G12B// phospholipase PLA2G12B NM_032562 0.0420214 2.20423 A2, group XIIB //10q22.1 // 84647 /// EN NM_021080 // DAB1 // disabled homolog 1 DAB1NM_021080 0.04076 2.20106 (Drosophila) // 1p32-p31 // 1600 /// ENSNM_001710 // CFB // complement factor B // CFB NM_001710 0.001816672.19954 6p21.3 // 629 /// ENST00000425368 // NM_183240 // TM EM37 //transmembrane TMEM37 NM_183240 0.0487149 2.19842 protein 37 // 2q14.2 //140738 /// ENST0000 AK127847 // FLJ45950 // FLJ45950 protein // FLJ45950AK127847 0.00195329 2.198 11q24.3 // 399975 NM_001710 // CFB //complement factor B // CFB NM_001710 0.00220919 2.19758 6p21.3 // 629/// ENST00000417261 // NM_144590 // ANKRD22 // ankyrin repeat ANKRD22NM_144590 0.0445105 2.19752 domain 22 // 10q23.31 // 118932 /// ENST0NM_002067 // GNA11 // guanine nucleotide GNA11 NM_002067 0.0140932.19185 binding protein (G protein), alpha 11 ( NM_006579 // EBP //emopamil binding EBP NM_006579 0.0115147 2.18786 protein (sterolisomerase) // Xp11.23-p11.2 NM_014873 // LPGAT1 // LPGAT1 NM_0148730.000550666 2.18469 lysophosphatidylglycerol acyltransferase 1 // 1q32// 992 NM_030943 // AMN // amnionless homolog AMN NM_030943 0.001688112.18289 (mouse) // 14q32.3 // 81693 /// ENST00000 NM_016548 // GOLM1 //golgi membrane GOLM1 NM_016548 0.0424472 2.18243 protein 1 // 9q21.33 //51280 /// NM_177937 NM_032148 // SLC41A2 // solute carrier SLC41A2NM_032148 0.0301277 2.17752 family 41, member 2 // 12q23.3 // 84102/NM_000949 // PRLR // prolactin receptor // PRLR NM_000949 0.03136492.17608 5p13.2 // 5618 /// ENST00000382002 // NM_181642 // SPINT1 //serine peptidase SPINT1 NM_181642 0.0361797 2.17498 inhibitor, Kunitztype 1 // 15q15.1 // 6 NM_001113567 // C17orf76 // chromosome C17orf76NM_001113567 0.0248369 2.17219 17 open reading frame 76 // 17p11.2 // 38NM_000355 // TCN2 // transcobalamin II // TCN2 NM_000355 0.02332792.17134 22q12.2 // 6948 /// NM_001184726 // TC NM_015198 // COBL //cordon-bleu COBL NM_015198 0.0208672 2.1656 homolog (mouse) // 7p12.1 //23242 /// ENST0000 NM_024616 // C3orf52 // chromosome 3 C3orf52NM_024616 0.00881101 2.16302 open reading frame 52 // 3q13.2 // 79669 //NM_020469 // ABO // ABO blood group ABO NM_020469 0.00222828 2.16292(transferase A, alpha 1-3-N-acetylgalactosam NM_030908 // OR2A4 //olfactory receptor, OR2A4 NM_030908 0.00568966 2.15894 family 2,subfamily A, member 4 // 6q2 NM_003980 // MAP7 // microtubule- MAP7NM_003980 0.0037529 2.15742 associated protein 7 // 6q23.3 // 9053 ///NM_0 NM_017417 // GALNT8 // UDP-N-acetyl- GALNT8 NM_017417 0.0136962.15417 alpha-D-galactosamine: polypeptide N-acetylga NM_005410 // SEPP1// selenoprotein P, SEPP1 NM_005410 0.0133071 2.15347 plasma, 1 // 5q31// 6414 /// NM_00108548 NM_152573 // RASEF // RAS and EF-hand RASEFNM_152573 0.0366785 2.15133 domain containing // 9q21.32 // 158158 ///NM_006633 // IQGAP2 // IQ motif containing IQGAP2 NM_006633 0.009698492.1509 GTPase activating protein 2 // 5q13.3 NM_152550 // SH3RF2 // SH3domain SH3RF2 NM_152550 0.00614396 2.15072 containing ring finger 2 //5q32 // 153769 /// NM_018686 // CMAS // cytidine CMAS NM_0186860.0124234 2.14998 monophosphate N-acetylneuraminic acid synthetase/NM_025045 // BAIAP2L2 // BA11-associated BAIAP2L2 NM_025045 0.01291622.14195 protein 2-like 2 // 22q13.1 // 80115 // NM_001859 // SLC31A1 //solute carrier SLC31A1 NM_001859 0.00838827 2.13821 family 31 (coppertransporters), member 1 NM_016614 // TDP2 // tyrosyl-DNA TDP2 NM_0166140.0246156 2.13573 phosphodiesterase 2 // 6p22.3-p22.1 // 51567 //NM_003848 // SUCLG2 // succinate-CoA SUCLG2 NM_003848 0.00569037 2.13077ligase, GDP-forming, beta subunit // 3p14.1 NM_017904 // TTC22 //tetratricopeptide TTC22 NM_017904 0.0153126 2.12827 repeat domain 22 //1p32.3 // 55001 /// NM_003060 // SLC22A5 // solute carrier SLC22A5NM_003060 0.02024 2.12394 family 22 (organic cation/carnitine transNM_002662 // PLD1 // phospholipase D1, PLD1 NM_002662 0.0135876 2.12113phosphatidylcholine-specific // 3q26 // 5 NM_018964 // SLC37A1 // solutecarrier SLC37A1 NM_018964 0.0229039 2.12062 family 37(glycerol-3-phosphate transport NM_001251 // CD68 // CD68molecule //CD68 NM_001251 0.00105743 2.11575 17p13 // 968 /// NM_001040059 // CD68// C NM_174941 // CD163L1 // CD163 molecule- CD163L1 NM_1749410.00407203 2.11396 like 1 // 12p13.3 // 283316 /// ENST00000 NM_016029// DHRS7 // DHRS7 NM_016029 0.0124063 2.11159 dehydrogenase/reductase(SDR family) member 7 // 14q23.1/ NM_024101 // MLPH // melanophilin //MLPH NM_024101 0.00197625 2.10533 2q37.3 // 79083 /// NM_001042467 //MLPH // NM_004670 // PAPSS2 // 3′- PAPSS2 NM_004670 0.0403309 2.10272phosphoadenosine 5′-phosphosulfate synthase 2 // 10q24 AK172782 // GPAM// glycerol-3-phosphate GPAM AK172782 0.0314353 2.09633 acyltransferase,mitochondrial // 10q25 NM_001142685 // ARHGAP32 // Rho ARHGAP32NM_001142685 0.00415504 2.09203 GTPase activating protein 32 // 11q24.3// 9743 NM_198495 // CTAGE4 // CTAGE family, CTAGE4 NM_198495 0.001413212.0906 member 4 // 7q35 // 100128553 /// NM_001145 ENST00000439698 //P4HA2 // prolyl 4- P4HA2 ENST00000439698 0.0142839 2.08741 hydroxylase,alpha polypeptide II // 5q31/ NM_015020 // PHLPP2 // PH domain andPHLPP2 NM_015020 0.013905 2.08634 leucine rich repeat proteinphosphatase 2/ NM_004252 // SLC9A3R1 // solute carrier SLC9A3R1NM_004252 0.00776993 2.0857 family 9 (sodium/hydrogen exchanger), meNM_012243 // SLC35A3 // solute carrier SLC35A3 NM_012243 0.03071012.07986 family 35 (UDP-N-acetylglucosamine (UDP-G NM_020184 // CNNM4 //cyclin M4 // 2q11 // CNNM4 NM_020184 0.02685 2.07897 26504 ///ENST00000377075 // CNNM4 // NM_001490 // GCNT1 // glucosaminyl (N- GCNT1NM_001490 0.00172819 2.07671 acetyl) transferase 1, core 2 // 9q13 // 2NM_003667 // LGR5 // leucine-rich repeat- LGR5 NM_003667 0.02375742.07254 containing G protein-coupled receptor 5 NM_001966 // EHHADH //enoyl-CoA, EHHADH NM_001966 0.0130422 2.07114 hydratase/3-hydroxyacylCoA dehydrogenase // 3 NM_017726 // PPP1R14D // protein PPP1R14DNM_017726 0.0497008 2.07017 phosphatase 1, regulatory (inhibitor)subunit 1 NM_006994 // BTN3A3 // butyrophilin, BTN3A3 NM_0069940.00121808 2.06925 subfamily 3, member A3 // 6p21.3 // 10384/NM_001039724 // NOSTRIN // nitric oxide NOSTRIN NM_001039724 0.009863432.06731 synthase trafficker // 2q31.1 // 115677 NR_026912 // ABHD11 //abhydrolase ABHD11 NR_026912 0.000593971 2.05896 domain containing 11 //7q11.23 // 83451 /// NM_001145206 // KIAA1671 // KIAA1671 // KIAA1671NM_001145206 0.00446756 2.05612 22q11.23 // 85379 /// ENST00000358431 //NM_153345 // TM EM 139 // transmembrane TMEM139 NM_153345 0.005053022.05293 protein 139 // 7q34 // 135932 /// ENST0000 NM_001164694 // IYD// iodotyrosine IYD NM_001164694 0.022189 2.05208 deiodinase // 6q25.1// 389434 /// NM_203395 NM_016472 // C14orf 129 // chromosome 14C14orf129 NM_016472 0.048055 2.04519 open reading frame 129 // 14q32.2// 515 NM_001017402 // LAMB3 // laminin, beta 3 // LAMB3 NM_0010174020.0267716 2.04174 1q32 // 3914 /// NM_001127641 // LAM NM_004999 // MYO6// myosin VI // 6q13 // MYO6 NM_004999 0.00369349 2.04095 4646 ///ENST00000369977 // MYO6 // my NR_027244 // LOC151009 // hypotheticalLOC151009 NR_027244 0.0115721 2.04078 LOC151009 // 2q13 // 151009 ///NR_027244 AB065085 // TOM1L1 // target of myb1 TOM1L1 AB065085 0.046562.03713 (chicken)-like 1 // 17q23.2 // 10040 NM_017750 // RETSAT //retinol saturase RETSAT NM_017750 0.0184264 2.03345 (all-trans-retinol13,14-reductase) // 2 NM_004721 // MAP3K13 // mitogen- MAP3K13 NM_0047210.00937615 2.03148 activated protein kinase kinase kinase 13 // 3q2NM_018677 // ACSS2 // acyl-CoA ACSS2 NM_018677 0.0306269 2.02661synthetase short-chain family member 2 // 20q11.2 NM_014317 // PDSS1 //prenyl (decaprenyl) PDSS1 NM_014317 0.0365076 2.02171 diphosphatesynthase, subunit 1 // 10p NM_014498 // GOLIM4 // golgi integral GOLIM4NM_014498 0.00240934 2.02056 membrane protein 4 // 3q26.2 // 27333 ///NM_033429 // CALML4 // calmodulin-like 4 // CALML4 NM_033429 0.04197842.01981 15q23 // 91860 /// NM_001031733 // C NR_036751 // HSP90AA6P //heat shock HSP90AA6P NR_036751 0.0220954 2.01604 protein 90 kDa alpha(cytosolic), class A me NM_012120 // CD2AP // CD2-associated CD2APNM_012120 0.00502091 2.0122 protein // 6p12 // 23607 /// ENST0000035931NM_005536 // IMPA1 // inositol(myo)-1 (or IMPA1 NM_005536 0.01946882.01203 4)-monophosphatase 1 // 8q21.13-q21.3/ NM_001153 // ANXA4 //annexinA4 // 2p13 // ANXA4 NM_001153 0.0255723 2.01151 307 ///ENST00000394295 // ANXA4 // NM_000147 // FUCA1 // fucosidase, alpha-FUCA1 NM_000147 0.00469253 2.0105 L-1, tissue // 1p34 // 2517 ///ENST000 NM_003774 // GALNT4 // UDP-N-acetyl- GALNT4 NM_003774 0.006223162.00871 alpha-D-galactosamine: polypeptide N- acetylga NM_001122890 //GGT6 // gamma- GGT6 NM_001122890 0.0328357 2.00627 glutamyltransferase 6// 17p13.2 // 124975 /// NM_ NM_001164277 // SLC37A4 // solute carrierSLC37A4 NM_001164277 0.0068184 2.00477 family 37 (glucose-6-phosphatetranspo NM_001565 // CXCL10 // chemokine (C-X-C CXCL10 NM_0015650.0468134 2.00368 motif) ligand 10 // 4q21 // 3627 /// ENS NM_005030 //PLK1 // polo-like kinase 1 // PLK1 NM_005030 0.0109795 2.00251 16p12.2// 5347 /// ENST00000300093/ NM_001012631 // IL32 // interleukin 32 //IL32 NM_001012631 0.0214868 2.00238 16p13.3 // 9235 /// NM_004221 //IL32 NM_005309 // GPT // glutamic-pyruvate GPT NM_005309 0.00982542.00201 transaminase (alanine aminotransferase) // NM_005159 // ACTC1 //actin, alpha, ACTC1 NM_005159 0.00451989 −2.00712 cardiac muscle 1 //15q11 -q14 // 70 /// ENST NM_130385 // MRVI1 // murine retrovirus MRVI1NM_130385 0.0186352 −2.00908 integration site 1 homolog // 11p15 // 1NR_003329 // SNORD116-14 // small SNORD116-14 NR_003329 0.00710694−2.01066 nucleolar RNA, C/D box 116-14 // 15q11.2 // 10 NM_030751 //ZEB1 // zinc finger E-box ZEB1 NM_030751 0.0190641 −2.01665 bindinghomeobox 1 // 10p11.2 // 6935 /// NM_001321 // CSRP2 // cysteine andCSRP2 NM_001321 0.0130189 −2.01975 glycine-rich protein 2 // 12q21.1 //1466 /// NM_199460 // CACNA1C // calcium CACNA1C NM_199460 0.0164629−2.03364 channel, voltage-dependent, L type, alpha 1C sub NM_007078 //LDB3 // LIM domain binding 3 // LDB3 NM_007078 0.013344 −2.0363610q22.3-q23.2 // 11155 /// NM_00117 ENST00000436525 // C15orf51 //dynamin 1 C15orf51 ENST00000436525 0.0479813 −2.04311 pseudogene //15q26.3 // 196968 ENST00000436525 // C15orf51 // dynamin 1 C15orf51ENST00000436525 0.0479813 −2.04311 pseudogene // 15q26.3 // 196968NM_001042454 // TGFB111 // transforming TGFB1I1 NM_001042454 0.0141045−2.0503 growth factor beta 1 induced transcript NM_201266 // NRP2 //neuropilin 2 // 2q33.3 // NRP2 NM_201266 0.0231808 −2.05329 8828 ///NM_003872 // NRP2 // neu NM_014286 // NCS1 // neuronal calcium NCS1NM_014286 0.0400809 −2.05571 sensor 1 // 9q34 // 23413 /// NM_001128826NR_002960 // SNORA20 // small nucleolar SNORA20 NR_002960 0.0102255−2.05618 RNA, H/ACA box 20 // 6q25.3 // 677806 NR_023343 // RNU4ATAC //RNA, U4atac RNU4ATAC NR_023343 0.0114016 −2.05953 small nuclear(U12-dependent splicing) // 2 NM_003829 // MPDZ // multiple PDZ MPDZNM_003829 0.0230169 −2.06542 domain protein // 9p23 // 8777 ///ENST0000038 NM_182734 // PLCB1 // phospholipase C, PLCB1 NM_1827340.0285626 −2.0675 beta 1 (phosphoinositide-specific) // 20p NM_212482 //FN1 // fibronectin 1 // 2q34 // FN1 NM_212482 0.0289963 −2.06817 2335/// NM_002026 // FN1 // fibron NM_001166292 // PTCH2 // patched 2 //PTCH2 NM_001166292 0.0155977 −2.06949 1p34.1 // 8643 /// ENST00000438067// PTCH NM_001128310 // SPARCL1 // SPARC-like SPARCL1 NM_0011283100.0275433 −2.0695 1 (hevin) // 4q22.1 // 8404 /// NM_004684 NR_003332 //SNORD116-17 // small SNORD116-17 NR_003332 0.00123218 −2.07085 nucleolarRNA, C/D box 116-17 // 15q11.2 // 10 NR_003332 // SNORD116-17 // smallSNORD116-17 NR_003332 0.00123218 −2.07085 nucleolar RNA, C/D box 116-17// 15q11.2 // 10 NM_001390 // DTNA // dystrobrevin, alpha // DTNANM_001390 0.0140008 −2.07227 18q12 // 1837 /// NM_032975 // DTNANM_172316 // MEIS2 // Meis homeobox 2 // MEIS2 NM_172316 0.012629−2.07482 15q14 // 4212 /// NM_170677 // MEIS2 // NM_032801 // JAM3 //junctional adhesion JAM3 NM_032801 0.00375191 −2.08055 molecule 3 //11q25 // 83700 /// ENST00 NM_001496 // GFRA3 // GDNF family GFRA3NM_001496 0.0143176 −2.08436 receptor alpha 3 // 5q31.1-q31.3 // 2676/// E NM_003116 // SPAG4 // sperm associated SPAG4 NM_003116 0.0370178−2.09743 antigen 4 // 20q11.21 // 6676 /// ENST000 NR_002754 // RNU5E //RNA, U5E small RNU5E NR_002754 0.0153145 −2.10499 nuclear // 1p36.22 //26829 /// M77839 // R NM_000109 // DM D // dystrophin // Xp21.2 // DMDNM_000109 0.0305823 −2.10535 1756 /// NM_004010 // DMD // dystropNM_005725 // TSPAN2 // tetraspanin 2 // TSPAN2 NM_005725 0.00484522−2.10726 1p13.2 // 10100 /// ENST00000369516 // T ENST00000436525 //C15orf51 // dynamin 1 C15orf51 ENST00000436525 0.0401346 −2.11861pseudogene // 15q26.3 // 196968 NM_001190839 // MGP // matrix Giaprotein // MGP NM_001190839 0.0229696 −2.13146 12p12.3 // 4256 ///NM_000900 // MG NM_031442 // TMEM47 // transmembrane TMEM47 NM_0314420.0162367 −2.16059 protein 47 // Xp11.4 // 83604 /// ENST00000 NM_002776// KLK10 // kallikrein-related KLK10 NM_002776 0.0131782 −2.16442peptidase 10 // 19q13 // 5655 /// NM_14 NM_134269 // SMTN // smoothelin// SMTN NM_134269 0.0278447 −2.16615 22q12.2 // 6525 /// NM_134270 //SMTN // smoo NM_002742 // PRKD1 // protein kinase D1 // PRKD1 NM_0027420.0208525 −2.17797 14q11 // 5587 /// ENST00000331968 // NM_001001396 //ATP2B4 // ATPase, Ca++ ATP2B4 NM_001001396 0.0372252 −2.18014transporting, plasma membrane 4 // 1q32.1 NM_005451 // PDLIM7 // PDZ andLIM PDLIM7 NM_005451 0.00654348 −2.18595 domain 7 (enigma) // 5q35.3 //9260 /// NM_20 NR_002952 // SNORA9 // small nucleolar SNORA9 NR_0029520.0244704 −2.19918 RNA, H/ACA box 9 // 7p13 // 677798 /// AK NM_003069// SMARCA1 // SWI/SNF SMARCA1 NM_003069 0.00571381 −2.2109 related,matrix associated, actin dependent regu NR_003330 // SNORD116-15 //small SNORD116-15 NR_003330 6.72E−05 −2.21218 nucleolar RNA, C/D box116-15 // 15q11.2 // 10 NM_002398 // MEIS1 // Meis homeobox 1 // MEIS1NM_002398 0.0208728 −2.21341 2p14 // 4211 /// ENST00000272369 // MEIENST00000436525 // C15orf51 // dynamin 1 C15orf51 ENST000004365250.0297132 −2.22015 pseudogene // 15q26.3 // 196968 ENST00000436525 //C15orf51 // dynamin 1 C15orf51 ENST00000436525 0.0297132 −2.22015pseudogene // 15q26.3 // 196968 NM_003734 // AOC3 // amine oxidase, AOC3NM_003734 0.0151647 −2.22019 copper containing 3 (vascular adhesionprote AF391113 // C21orf70 // chromosome 21 C21orf70 AF391113 0.00109586−2.22308 open reading frame 70 // 21q22.3 // 85395 NM_001937 // DPT //dermatopontin // 1q12- DPT NM_001937 0.0379186 −2.22359 q23 // 1805 ///ENST00000367817 // DPT NM_012232 // PTRF // polymerase I and PTRFNM_012232 0.0194925 −2.23107 transcript release factor // 17q21.2 // 28NM_024605 // ARHGAP10 // Rho GTPase ARHGAP10 NM_024605 0.00832518−2.23204 activating protein 10 // 4q31.23 // 79658 // NM_022117 //TSPYL2 // TSPY-like2 // TSPYL2 NM_022117 0.0134024 −2.23502 Xp11.2 //64061 /// ENST00000375442 // TSP NM_005100 // AKAP12 // A kinase (PRKA)AKAP12 NM_005100 0.0357306 −2.24089 anchor protein 12 // 6q24-q25 //9590 /// AY423733 // DDR2 // discoidin domain DDR2 AY423733 0.0358613−2.2447 receptor tyrosine kinase 2 // 1q23.3 // 492 NM_153703 // PODN //podocan // 1p32.3 // PODN NM_153703 0.0277365 −2.26923 127435 ///ENST00000312553 // PODN // NM_004370 // COL12A1 // collagen, typeCOL12A1 NM_004370 0.0499701 −2.27002 XII, alpha 1 // 6q12-q13 // 1303/// NM_0 NM_004137 // KCNMB1 // potassium large KCNMB1 NM_0041370.0277682 −2.27584 conductance calcium-activated channel, su NM_014575// SCHIP1 // schwannomin SCHIP1 NM_014575 0.00470657 −2.28272interacting protein 1 // 3q25.32-q25.33 // 29 NM_001753 // CAV1 //caveolin 1, caveolae CAV1 NM_001753 0.0368534 −2.29054 protein, 22 kDa// 7q31.1 // 857 /// NM NM_002338 // LSAMP // limbic system- LSAMPNM_002338 0.0456749 −2.30408 associated membrane protein // 3q13.2-q21// NM_058229 // FBXO32 // F-box protein 32 // FBXO32 NM_058229 0.0422526−2.30763 8q24.13 // 114907 /// NM_148177 // FB NM_006765 // TUSC3 //tumor suppressor TUSC3 NM_006765 0.00173576 −2.32217 candidate 3 // 8p22// 7991 /// NM_178234 NM_015687 // FILIP1 // filamin A interactingFILIP1 NM_015687 0.0158717 −2.32321 protein 1 // 6q14.1 // 27145 /// ENNM_006080 // SEMA3A // sema domain, SEMA3A NM_006080 0.0142131 −2.32699immunoglobulin domain (Ig), short basic doma NM_000922 // PDE3B //phosphodiesterase PDE3B NM_000922 0.00420057 −2.33135 3B, cGMP-inhibited// 11p15.1 // 5140 // NM_000722 // CACNA2D1 // calcium CACNA2D1NM_000722 0.0107345 −2.33411 channel, voltage-dependent, alpha 2/deltasubun NM_001197294 // DPYSL3 // dihydropyrimidinase- DPYSL3 NM_0011972940.0231385 −2.33517 like 3 // 5q32 // 1809 /// NM_0013 NM_172311 //STON1-GTF2A1L // STON1- TON1-GTF2A1 NM_172311 0.0264382 −2.33729 GTF2A1Lreadthrough // 2p16.3 // 286749 /// NM_000857 // GUCY1B3 // guanylateGUCY1B3 NM_000857 0.0141507 −2.34285 cyclase 1, soluble, beta 3 //4q31.3-q33 // 29 NR_033662 // CSF3 // colony stimulating CSF3 NR_0336620.036854 −2.35397 factor 3 (granulocyte) // 17q11.2-q12 // NM_001706 //BCL6 // B-cell CLL/lymphoma BCL6 NM_001706 0.0395014 −2.37213 6 // 3q27// 604 /// NM_001130845 // BC NM_014112 // TRPS1 //trichorhinophalangeal TRPS1 NM_014112 0.021813 −2.37338 syndrome I //8q24.12 // 7227 /// EN NM_003275 // TMOD1 // tropomodulin 1 // TMOD1NM_003275 0.00926909 −2.39163 9q22.3 // 7111 /// NM_001166116 // TMOD1NM_004040 // RHOB // ras homolog gene RHOB NM_004040 0.00209611 −2.39166family, member B // 2p24 // 388 /// ENST00 NM_007281 // SCRG1 //stimulator of SCRG1 NM_007281 0.0449505 −2.42771 chondrogenesis 1 //4q34.1 // 11341 /// ENST NM_053025 // MYLK // myosin light chain MYLKNM_053025 0.0334323 −2.44896 kinase // 3q21 // 4638 /// NM_053026 //NM_133646 // ZAK // sterile alpha motif and ZAK NM_133646 0.0101002−2.45225 leucine zipper containing kinase AZK NM_001123364 // C6orf 186// chromosome C6orf186 NM_001123364 0.0338175 −2.45305 6 open readingframe 186 // 6q21 // 72846 NM_005909 // MAPI B // microtubule- MAP1BNM_005909 0.00199713 −2.45363 associated protein 1B // 5q13 // 4131 ///ENST NM_001136191 // KANK2 // KN motif and KANK2 NM_001136191 0.00418−2.45823 ankyrin repeat domains 2 // 19p13.2 // 259 NR_002836 // PGM5P2// phosphoglucomutase PGM5P2 NR_002836 0.0106051 −2.46207 5 pseudogene 2// 9q12 // 595135 /// N NM_006988 // ADAMTS1 // ADAM ADAMTS1 NM_0069880.0212926 −2.47602 metallopeptidase with thrombospondin type 1 motif,NM_001897 // CSPG4 // chondroitin sulfate CSPG4 NM_001897 0.000233664−2.47738 proteoglycan 4 // 15q24.2 // 1464 /// NM_012134 // LMOD1 //leiomodin 1 LMOD1 NM_012134 0.0254164 −2.48821 (smooth muscle) // 1q32// 25802 /// ENST00000 NM_000856 // GUCY1A3 // guanylate GUCY1A3NM_000856 0.0154068 −2.49669 cyclase 1, soluble, alpha 3 //4q31.3-q33|4q31 NR_002196 // H19 // H19, imprinted H19 NR_0021960.0422207 −2.49895 maternally expressed transcript (non-proteinNM_002667 // PLN // phospholamban // PLN NM_002667 0.0458219 −2.505286q22.1 // 5350 /// ENST00000357525 // PLN/ NM_004078 // CSRP1 //cysteine and CSRP1 NM_004078 0.0389579 −2.51599 glycine-rich protein 1// 1q32 // 1465 /// NM NM_001141945 // ACTA2 // actin, alpha2, ACTA2NM_001141945 0.00367966 −2.51621 smooth muscle, aorta // 10q23.3 // 59/NM_002986 // CCL11 // chemokine(C-C CCL11 NM_002986 0.0132628 −2.5178motif) ligand 11 // 17q21.1-q21.2 // 6356/ NM_033138 // CALD1 //caldesmon 1 // CALD1 NM_033138 0.0229067 −2.51869 7q33 // 800 ///NM_033157 // CALD1 // calde NM_001164836 // FXYD6 // FXYD domain FXYD6NM_001164836 0.0202065 −2.53004 containing ion transport regulator 6 //11q NM_003725 // HSD17B6 // hydroxysteroid HSD17B6 NM_003725 0.0196889−2.54527 (17-beta) dehydrogenase 6 homolog (mouse) NM_001146312 // MYOCD// myocardin // MYOCD NM_001146312 0.0298805 −2.59465 17p11.2 // 93649/// NM_153604 // MYOCD // NM_015225 // PRUNE2 // prune homolog 2 PRUNE2NM_015225 0.0217217 −2.59492 (Drosophila) // 9q21.2 // 158471 /// AB53NM_001168278 // WWTR1 // WW domain WWTR1 NM_001168278 0.014475 −2.60243containing transcription regulator 1 // 3q23- NM_001008711 // RBPMS //RNA binding RBPMS NM_001008711 0.00600769 −2.60406 protein with multiplesplicing // 8p12 // 1 NM_001014796 // DDR2 // discoidin domain DDR2NM_001014796 0.00523497 −2.61121 receptor tyrosine kinase 2 // 1q23.3 //NM_018640 // LMO3 // UM domain only 3 LMO3 NM_018640 0.042971 −2.63105(rhombotin-like 2) // 12p12.3 // 55885 // NR_002836 // PGM5P2 //phosphoglucomutase PGM5P2 NR_002836 0.00678244 −2.64929 5 pseudogene 2// 9q12 // 595135 /// N NM_021914 // CFL2 // cofilin 2 (muscle) // CFL2NM_021914 0.0261349 −2.65343 14q12 // 1073 /// NM_138638 // CFL2/NM_016277 // RAB23 // RAB23, member RAB23 NM_016277 0.035448 −2.66122RAS oncogene family // 6p11 // 51715 /// NM_ NM_145234 // CHRDL1 //chordin-like 1 // CHRDL1 NM_145234 0.00265317 −2.67563 Xq23 // 91851 ///NM_001143981 // CHRDL NM_001134439 // PHLDB2 // pleckstrin PHLDB2NM_001134439 0.0258326 −2.67775 homology-like domain, family B, member 2// NM_006832 // FERMT2 // fermitin family FERMT2 NM_006832 0.0205617−2.7145 member 2 // 14q22.1 // 10979 /// NM_00113 NM_001128205 // SULF1// sulfatase 1 // SULF1 NM_001128205 0.0335496 −2.73234 8q13.1 // 23213/// NM_015170 // SULF1/ NM_194272 // RBPMS2 // RNA binding RBPMS2NM_194272 0.012053 −2.74286 protein with multiple splicing 2 // 15q22.31NM_014476 // PDLIM3 // PDZ and LIM PDLIM3 NM_014476 0.0110612 −2.7574domain 3 // 4q35 // 27295 /// NM_001114107 // NM_015886 // P115 //peptidase inhibitor 15 // PI15 NM_015886 0.0312943 −2.78937 8q21.11 //51050 /// ENST00000260 NM_003289 // TPM2 // tropomyosin 2 (beta) // TPM2NM_003289 0.0272347 −2.80338 9p13 // 7169 /// NM_213674 // TPM2NM_001458 // FLNC // filamin C, gamma // FLNC NM_001458 0.0113027−2.80588 7q32-q35 // 2318 /// NM_001127487 // FL NM_006097 // MYL9 //myosin, light chain 9, MYL9 NM_006097 0.0412118 −2.81849 regulatory //20q11.23 // 10398 /// NM_199460 // CACNA1C // calcium CACNA1C NM_1994600.00694625 −2.83404 channel, voltage-dependent, L type, alpha 1C subNM_001232 // CASQ2 // calsequestrin 2 CASQ2 NM_001232 0.0349505 −2.84886(cardiac muscle) // 1p13.3-p11 // 845 /// NM_001193460 // MSRB3 //methionine MSRB3 NM_001193460 0.0108076 −2.84899 sulfoxide reductase B3// 12q14.3 // 253827 NM_001456 // FLNA // filamin A, alpha // FLNANM_001456 0.0164878 −2.86026 Xq28 // 2316 /// NM_001110556 // FLNA/NM_006366 // CAP2 // CAP, adenylate CAP2 NM_006366 0.00596997 −2.89059cyclase-associated protein, 2 (yeast) // 6p2 NM_001031701 // NT5DC3 //5′- NT5DC3 NM_001031701 0.0464686 −2.90347 nucleotidase domaincontaining 3 // 12q22-q23.1 // NM_003999 // OSMR // oncostatin M OSMRNM_003999 0.0324297 −2.92605 receptor // 5p13.1 // 9180 /// NM_001168355// NM_001885 // CRYAB // crystallin, alpha B // CRYAB NM_0018850.0163674 −2.96044 11q22.3-q23.1 // 1410 /// ENST00000 NM_000517 // HBA2// hemoglobin, alpha 2 // HBA2 NM_000517 0.0195505 −3.10109 16p13.3 //3040 /// BC101846 // HBA1 NM_000558 // HBA1 // hemoglobin, alpha 1 //HBA1 NM_000558 0.0195505 −3.10109 16p13.3 // 3039 /// BC101846 // HBA1NM_004282 // BAG2 // BCL2-associated BAG2 NM_004282 0.0108668 −3.11097athanogene 2 // 6p12.1-p11.2 // 9532 /// EN NM_022135 // POPDC2 //popeye domain POPDC2 NM_022135 0.0219995 −3.1427 containing 2 // 3q13.33// 64091 /// ENST00 NM_001001522 // TAGLN // transgelin // TAGLNNM_001001522 0.0148609 −3.35842 11q23.2 // 6876 /// NM_003186 // TAGLN// NM_212482 // FN1 // fibronectin 1 // 2q34 // FN1 NM_212482 0.00987492−3.43741 2335 /// NM_002026 // FN1 // fibron NM_133477 // SYNPO2 //synaptopodin 2 // SYNPO2 NM_133477 0.0241716 −3.56252 4q26 // 171024 ///NM_001128933 // SYNP NM_000450 // SELE // selectin E // 1q22-q25 // SELENM_000450 0.0460446 −3.56423 6401 /// ENST00000333360 // SELE NR_029686// MIR145 // microRNA 145 // MIR145 NR_029686 0.0119026 −3.58867 5q32 //406937 /// NR_027180 // LOC728264 NM_022648 // TNS1 // tensin 1 //2q35-q36 // TNS1 NM_022648 0.00555851 −3.61273 7145 /// ENST00000171887// TNS1 // NM_001615 // ACTG2 // actin, gamma 2, ACTG2 NM_0016150.0379131 −3.62826 smooth muscle, enteric // 2p13.1 // 72 /// NM_022844// MYH11 // myosin, heavy MYH11 NM_022844 0.0240032 −3.66415 chain 11,smooth muscle // 16p13.11 // 4629 NM_002205 // ITGA5 // integrin, alpha5 ITGA5 NM_002205 0.0207749 −3.82521 (fibronectin receptor, alphapolypeptide NM_001299 // CNN1 // calponin 1, basic, CNN1 NM_0012990.0413103 −3.84711 smooth muscle // 19p13.2-p13.1 // 1264/ NM_001034954// SORBS1 // sorbin and SORBS1 NM_001034954 0.00399907 −3.89048 SH3domain containing 1 // 10q23.33 // 1058 NM_001927 // DES // desmin //2q35 // 1674 /// DES NM_001927 0.0268126 −3.90558 ENST00000373960 // DES// desmin NM_144617 // HSPB6 // heat shock protein, HSPB6 NM_1446170.0145209 −3.90993 alpha-crystallin-related, B6 // 19q13. NM_015424 //CHRDL2 // chordin-like 2 // CHRDL2 NM_015424 0.0247555 −4.23746 11q14 //25884 /// ENST00000263671 // C NM_000518 // HBB // hemoglobin, beta //HBB NM_000518 0.0255665 −4.3277 11p15.5 // 3043 /// ENST00000335295 // HNM_002160 // TNC // tenascin C // 9q33 // TNC NM_002160 0.0126641−4.4403 3371 /// ENST00000350763 // TNC // ten NM_006198 // PCP4 //Purkinje cell protein PCP4 NM_006198 0.0340302 −4.51736 4 // 21q22.2 //5121 /// ENST00000328

What is claimed is:
 1. A method of measuring HD5 in a patient sufferingfrom or at risk of inflammatory bowel disease (IBD), said methodcomprising: obtaining a sample from the patient; and measuring at leastone of an expression of HD5 and a concentration of HD5 in the sample. 2.A method of measuring MMP-7 in a patient suffering from or at risk ofinflammatory bowel disease (IBD), said method comprising: obtaining asample from the patient; and measuring at least one of the expression ofMMP-7 and the concentration of MMP-7 in the sample.
 3. A method oftreating a patient suffering from or at risk of inflammatory boweldisease (IBD), said method comprising: performing the method ofmeasuring MMP-7 in the patient according to claim 2; and performing anintervention on the patient to treat Crohn's disease.
 4. The method ofclaim 2, comprising: comparing the expression of MMP-7 or theconcentration of MMP-7 in the sample to a benchmark value that istypical of a subject not suffering from ulcerative colitis or severeulcerative colitis; and diagnosing Crohn's disease if the expression ofMMP-7 or the concentration of MMP-7 in the sample does not significantlyexceed the benchmark value.
 5. The method of claim 3, comprising:comparing the expression of MMP-7 or the concentration of MMP-7 in thesample to a benchmark value that is typical of a subject not sufferingfrom ulcerative colitis or severe ulcerative colitis; and diagnosingCrohn's disease if the expression of MMP-7 or the concentration of MMP-7in the sample does not significantly exceed the benchmark value.
 6. Themethod of claim 2, wherein the expression of MMP-7 or the concentrationof MMP-7 in the sample is below a benchmark value that is typical of asubject suffering from ulcerative colitis or severe ulcerative colitis.7. The method of claim 2, wherein the expression of MMP-7 is measured tobe significantly less in the sample than in a control sample from asubject suffering from ulcerative colitis or severe ulcerative colitis.8. The method of claim 2, wherein the expression of MMP-7 is measured inthe sample to be at most about 1/10 of the expression of MMP-7 measuredin a control sample from a subject not suffering from ulcerative colitisor severe ulcerative colitis.
 9. The method of claim 2, wherein thesample is intestinal tissue, and comprising measuring the concentrationof MMP-7 by: immunostaining the sample with an antiMMP-7 immunostainingagent; and measuring the percentage of cells in the sample that stainpositive.
 10. The method of claim 2, wherein the intervention is noteffective to treat ulcerative colitis or severe ulcerative colitis. 11.The method of claim 2, wherein the intervention is administration of adrug, to the exclusion of a surgery.
 12. The method of claim 2, whereinthe intervention is administration of a drug selected from the groupconsisting of: a vitamin supplement, vitamin B12, vitamin D, a mineralsupplement, calcium, an anti-inflammatory, a corticosteroid, a5-aminosalicylate, an immunosuppressant, azathioprine, mercaptopurine,an anti-TNF-alpha antibody, infliximab, adalimumab, certolizumab pegol,methotrexate, an anti-α4-integrin antibody, natalizumab, vedolizumab, ananti-interleukin antibody, ustekinumab, an antibacterial antibiotic,ciprofloxacin, and metronidazole.
 13. The method of claim 2, wherein theintervention is administration of a drug selected from the groupconsisting of: vitamin B12, vitamin D, calcium, certolizumab pegol,methotrexate, and natalizumab.
 14. The method of claim 2, wherein theintervention is placement of the subject on a low fat diet.
 15. A methodof treating a patient suffering from or at risk of inflammatory boweldisease (IBD), said method comprising: performing the method ofmeasuring MMP-7 in the patient according to claim 2; and performing anintervention on the patient to treat ulcerative colitis or severeulcerative colitis.
 16. The method of claim 2, comprising: comparing theexpression of MMP-7 or the concentration of MMP-7 in the sample to abenchmark value that is typical of a subject not suffering fromulcerative colitis or severe ulcerative colitis; and diagnosingulcerative colitis or severe ulcerative colitis if the expression ofMMP-7 or the concentration of MMP-7 in the sample significantly exceedsthe benchmark value.
 17. The method of claim 15, comprising: comparingthe expression of MMP-7 or the concentration of MMP-7 in the sample to abenchmark value that is typical of a subject not suffering fromulcerative colitis or severe ulcerative colitis; and diagnosingulcerative colitis or severe ulcerative colitis if the expression ofMMP-7 or the concentration of MMP-7 in the sample significantly exceedsthe benchmark value.
 18. The method of claim 15, wherein the sample isintestinal tissue, and comprising measuring the concentration of MMP-7by: immunostaining the sample with an anti-MMP-7 immunostaining agent;and measuring the percentage of cells in the sample that stain positive.19. The method of claim 15, wherein the intervention is not effective totreat Crohn's disease.
 20. The method of claim 15, wherein theintervention is a surgery selected from the group consisting of: aproctocolectomy, and an ileal pouch anal anastomosis.
 21. The method ofclaim 15, wherein the intervention is administration of a drug selectedfrom the group consisting of: an iron supplement, an anti-inflammatory,a corticosteroid, a 5-aminosalicylate, an immunosuppressant,azathioprine, mercaptopurine, cyclosporine, an anti-TNF-alpha antibody,infliximab, adalimumab, golimumab, methotrexate, an anti-α4-integrinantibody, vedolizumab, an antibacterial antibiotic, ciprofloxacin, andmetronidazole.
 22. The method of claim 15, wherein the intervention isadministration of a drug selected from the group consisting of:cyclosporine, and golimumab.
 23. A kit for measuring HD5 and MMP-7 in asample, the kit comprising: a first assay for measuring at least one ofthe expression of human HD5 and the concentration of human HD5 in asample; and a second assay for measuring at least one of the expressionof human MMP-7 and the concentration of human MMP-7 in a sample.